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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-26, 11:02 CST based on data in:

        General Statistics

        Showing 256/256 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        CR1304_17111FL-61-01-25_S119_L006_R1_001
        12.4%
        49%
        151bp
        14.0M
        CR1304_17111FL-61-01-25_S119_L006_R2_001
        12.8%
        48%
        151bp
        14.0M
        CR1304_17111FL-61-01-25_S119_L006_trimmed_1P
        12.0%
        47%
        151bp
        13.8M
        CR1304_17111FL-61-01-25_S119_L006_trimmed_2P
        12.3%
        47%
        151bp
        13.8M
        CR1305_17111FL-61-01-26_S120_L006_R1_001
        20.0%
        48%
        151bp
        16.0M
        CR1305_17111FL-61-01-26_S120_L006_R2_001
        20.2%
        46%
        151bp
        16.0M
        CR1305_17111FL-61-01-26_S120_L006_trimmed_1P
        19.0%
        43%
        117bp
        15.7M
        CR1305_17111FL-61-01-26_S120_L006_trimmed_2P
        19.4%
        43%
        117bp
        15.7M
        CR1306_17111FL-61-01-27_S121_L006_R1_001
        24.4%
        49%
        151bp
        13.9M
        CR1306_17111FL-61-01-27_S121_L006_R2_001
        24.6%
        47%
        151bp
        13.9M
        CR1306_17111FL-61-01-27_S121_L006_trimmed_1P
        23.3%
        45%
        127bp
        13.7M
        CR1306_17111FL-61-01-27_S121_L006_trimmed_2P
        23.6%
        45%
        127bp
        13.7M
        CR1307_17111FL-61-01-28_S122_L006_R1_001
        22.0%
        53%
        151bp
        17.3M
        CR1307_17111FL-61-01-28_S122_L006_R2_001
        22.2%
        50%
        151bp
        17.3M
        CR1307_17111FL-61-01-28_S122_L006_trimmed_1P
        20.9%
        47%
        102bp
        17.0M
        CR1307_17111FL-61-01-28_S122_L006_trimmed_2P
        21.3%
        47%
        102bp
        17.0M
        CR1308_17111FL-61-01-29_S123_L006_R1_001
        27.9%
        54%
        151bp
        19.8M
        CR1308_17111FL-61-01-29_S123_L006_R2_001
        28.5%
        50%
        151bp
        19.8M
        CR1308_17111FL-61-01-29_S123_L006_trimmed_1P
        26.7%
        48%
        97bp
        19.4M
        CR1308_17111FL-61-01-29_S123_L006_trimmed_2P
        27.3%
        48%
        97bp
        19.4M
        CR1309_17111FL-61-01-30_S124_L006_R1_001
        18.6%
        51%
        151bp
        14.6M
        CR1309_17111FL-61-01-30_S124_L006_R2_001
        19.0%
        48%
        151bp
        14.6M
        CR1309_17111FL-61-01-30_S124_L006_trimmed_1P
        17.8%
        46%
        117bp
        14.4M
        CR1309_17111FL-61-01-30_S124_L006_trimmed_2P
        18.3%
        46%
        117bp
        14.4M
        CR1310_17111FL-61-01-31_S125_L006_R1_001
        17.5%
        51%
        151bp
        13.8M
        CR1310_17111FL-61-01-31_S125_L006_R2_001
        17.6%
        49%
        151bp
        13.8M
        CR1310_17111FL-61-01-31_S125_L006_trimmed_1P
        16.7%
        46%
        122bp
        13.6M
        CR1310_17111FL-61-01-31_S125_L006_trimmed_2P
        17.0%
        46%
        122bp
        13.6M
        CR1311_17111FL-61-01-32_S126_L006_R1_001
        19.2%
        49%
        151bp
        14.8M
        CR1311_17111FL-61-01-32_S126_L006_R2_001
        19.5%
        48%
        151bp
        14.8M
        CR1311_17111FL-61-01-32_S126_L006_trimmed_1P
        18.2%
        46%
        117bp
        14.6M
        CR1311_17111FL-61-01-32_S126_L006_trimmed_2P
        18.6%
        46%
        117bp
        14.6M
        CR1312_17111FL-61-01-33_S127_L006_R1_001
        12.6%
        51%
        151bp
        13.6M
        CR1312_17111FL-61-01-33_S127_L006_R2_001
        12.8%
        49%
        151bp
        13.6M
        CR1312_17111FL-61-01-33_S127_L006_trimmed_1P
        12.1%
        48%
        151bp
        13.5M
        CR1312_17111FL-61-01-33_S127_L006_trimmed_2P
        12.3%
        48%
        151bp
        13.5M
        CR1313_17111FL-61-01-34_S128_L006_R1_001
        19.1%
        53%
        151bp
        16.3M
        CR1313_17111FL-61-01-34_S128_L006_R2_001
        19.3%
        50%
        151bp
        16.3M
        CR1313_17111FL-61-01-34_S128_L006_trimmed_1P
        17.8%
        47%
        97bp
        16.1M
        CR1313_17111FL-61-01-34_S128_L006_trimmed_2P
        18.1%
        47%
        97bp
        16.1M
        CR1314_17111FL-61-01-35_S129_L006_R1_001
        22.0%
        56%
        151bp
        16.3M
        CR1314_17111FL-61-01-35_S129_L006_R2_001
        22.3%
        51%
        151bp
        16.3M
        CR1314_17111FL-61-01-35_S129_L006_trimmed_1P
        20.2%
        49%
        97bp
        16.0M
        CR1314_17111FL-61-01-35_S129_L006_trimmed_2P
        20.5%
        49%
        97bp
        16.0M
        CR1315_17111FL-61-01-36_S130_L006_R1_001
        21.6%
        53%
        151bp
        16.6M
        CR1315_17111FL-61-01-36_S130_L006_R2_001
        21.9%
        49%
        151bp
        16.6M
        CR1315_17111FL-61-01-36_S130_L006_trimmed_1P
        20.3%
        47%
        102bp
        16.3M
        CR1315_17111FL-61-01-36_S130_L006_trimmed_2P
        20.7%
        47%
        102bp
        16.3M
        CR1316_17111FL-61-01-37_S131_L006_R1_001
        14.5%
        52%
        151bp
        13.2M
        CR1316_17111FL-61-01-37_S131_L006_R2_001
        14.7%
        48%
        151bp
        13.2M
        CR1316_17111FL-61-01-37_S131_L006_trimmed_1P
        13.6%
        46%
        107bp
        13.0M
        CR1316_17111FL-61-01-37_S131_L006_trimmed_2P
        13.9%
        46%
        107bp
        13.0M
        CR1317_17111FL-61-01-38_S132_L006_R1_001
        14.5%
        49%
        151bp
        12.4M
        CR1317_17111FL-61-01-38_S132_L006_R2_001
        14.6%
        47%
        151bp
        12.4M
        CR1317_17111FL-61-01-38_S132_L006_trimmed_1P
        13.7%
        45%
        122bp
        12.3M
        CR1317_17111FL-61-01-38_S132_L006_trimmed_2P
        13.9%
        45%
        122bp
        12.3M
        CR1318_17111FL-61-01-39_S133_L006_R1_001
        17.1%
        50%
        151bp
        14.0M
        CR1318_17111FL-61-01-39_S133_L006_R2_001
        17.3%
        48%
        151bp
        14.0M
        CR1318_17111FL-61-01-39_S133_L006_trimmed_1P
        16.2%
        46%
        112bp
        13.8M
        CR1318_17111FL-61-01-39_S133_L006_trimmed_2P
        16.4%
        46%
        112bp
        13.8M
        CR1319_17111FL-61-01-40_S134_L006_R1_001
        16.7%
        52%
        151bp
        12.5M
        CR1319_17111FL-61-01-40_S134_L006_R2_001
        16.9%
        48%
        151bp
        12.5M
        CR1319_17111FL-61-01-40_S134_L006_trimmed_1P
        15.7%
        47%
        112bp
        12.3M
        CR1319_17111FL-61-01-40_S134_L006_trimmed_2P
        15.9%
        47%
        112bp
        12.3M
        CR1320_17111FL-61-01-41_S135_L006_R1_001
        11.9%
        51%
        151bp
        15.5M
        CR1320_17111FL-61-01-41_S135_L006_R2_001
        12.2%
        50%
        151bp
        15.5M
        CR1320_17111FL-61-01-41_S135_L006_trimmed_1P
        11.5%
        50%
        151bp
        15.4M
        CR1320_17111FL-61-01-41_S135_L006_trimmed_2P
        11.8%
        50%
        151bp
        15.4M
        CR1321_17111FL-61-01-42_S136_L006_R1_001
        16.9%
        51%
        151bp
        17.2M
        CR1321_17111FL-61-01-42_S136_L006_R2_001
        17.2%
        49%
        151bp
        17.2M
        CR1321_17111FL-61-01-42_S136_L006_trimmed_1P
        16.1%
        47%
        112bp
        17.0M
        CR1321_17111FL-61-01-42_S136_L006_trimmed_2P
        16.4%
        46%
        112bp
        17.0M
        CR1322_17111FL-61-01-43_S137_L006_R1_001
        23.2%
        50%
        151bp
        16.3M
        CR1322_17111FL-61-01-43_S137_L006_R2_001
        23.4%
        48%
        151bp
        16.3M
        CR1322_17111FL-61-01-43_S137_L006_trimmed_1P
        22.3%
        46%
        127bp
        16.1M
        CR1322_17111FL-61-01-43_S137_L006_trimmed_2P
        22.6%
        46%
        127bp
        16.1M
        CR1323_17111FL-61-01-44_S138_L006_R1_001
        12.9%
        48%
        151bp
        12.7M
        CR1323_17111FL-61-01-44_S138_L006_R2_001
        13.0%
        46%
        151bp
        12.7M
        CR1323_17111FL-61-01-44_S138_L006_trimmed_1P
        12.3%
        44%
        122bp
        12.6M
        CR1323_17111FL-61-01-44_S138_L006_trimmed_2P
        12.4%
        44%
        122bp
        12.6M
        CR1324_17111FL-61-01-45_S139_L006_R1_001
        16.3%
        47%
        151bp
        15.4M
        CR1324_17111FL-61-01-45_S139_L006_R2_001
        16.5%
        46%
        151bp
        15.4M
        CR1324_17111FL-61-01-45_S139_L006_trimmed_1P
        15.8%
        44%
        137bp
        15.3M
        CR1324_17111FL-61-01-45_S139_L006_trimmed_2P
        16.1%
        44%
        137bp
        15.3M
        CR1325_17111FL-61-01-46_S140_L006_R1_001
        15.8%
        47%
        151bp
        13.9M
        CR1325_17111FL-61-01-46_S140_L006_R2_001
        16.0%
        46%
        151bp
        13.9M
        CR1325_17111FL-61-01-46_S140_L006_trimmed_1P
        15.3%
        44%
        142bp
        13.8M
        CR1325_17111FL-61-01-46_S140_L006_trimmed_2P
        15.5%
        44%
        142bp
        13.8M
        CR1326_17111FL-61-01-47_S141_L006_R1_001
        24.0%
        51%
        151bp
        15.1M
        CR1326_17111FL-61-01-47_S141_L006_R2_001
        24.2%
        50%
        151bp
        15.1M
        CR1326_17111FL-61-01-47_S141_L006_trimmed_1P
        23.4%
        48%
        122bp
        14.9M
        CR1326_17111FL-61-01-47_S141_L006_trimmed_2P
        23.6%
        48%
        122bp
        14.9M
        CR1327_17111FL-61-01-48_S142_L006_R1_001
        18.8%
        51%
        151bp
        12.6M
        CR1327_17111FL-61-01-48_S142_L006_R2_001
        19.0%
        49%
        151bp
        12.6M
        CR1327_17111FL-61-01-48_S142_L006_trimmed_1P
        18.1%
        47%
        117bp
        12.4M
        CR1327_17111FL-61-01-48_S142_L006_trimmed_2P
        18.3%
        47%
        117bp
        12.4M
        CR1328_17111FL-61-01-49_S143_L006_R1_001
        11.3%
        51%
        151bp
        15.0M
        CR1328_17111FL-61-01-49_S143_L006_R2_001
        11.6%
        49%
        151bp
        15.0M
        CR1328_17111FL-61-01-49_S143_L006_trimmed_1P
        11.0%
        49%
        151bp
        14.8M
        CR1328_17111FL-61-01-49_S143_L006_trimmed_2P
        11.3%
        49%
        151bp
        14.8M
        CR1329_17111FL-61-01-50_S144_L006_R1_001
        13.3%
        48%
        151bp
        15.5M
        CR1329_17111FL-61-01-50_S144_L006_R2_001
        13.5%
        46%
        151bp
        15.5M
        CR1329_17111FL-61-01-50_S144_L006_trimmed_1P
        12.6%
        44%
        122bp
        15.4M
        CR1329_17111FL-61-01-50_S144_L006_trimmed_2P
        12.9%
        44%
        122bp
        15.4M
        CR1330_17111FL-61-01-51_S145_L006_R1_001
        18.4%
        49%
        151bp
        14.0M
        CR1330_17111FL-61-01-51_S145_L006_R2_001
        18.6%
        47%
        151bp
        14.0M
        CR1330_17111FL-61-01-51_S145_L006_trimmed_1P
        17.6%
        45%
        122bp
        13.9M
        CR1330_17111FL-61-01-51_S145_L006_trimmed_2P
        17.8%
        45%
        122bp
        13.9M
        CR1331_17111FL-61-01-52_S146_L006_R1_001
        13.5%
        49%
        151bp
        17.1M
        CR1331_17111FL-61-01-52_S146_L006_R2_001
        13.6%
        47%
        151bp
        17.1M
        CR1331_17111FL-61-01-52_S146_L006_trimmed_1P
        12.7%
        44%
        112bp
        16.9M
        CR1331_17111FL-61-01-52_S146_L006_trimmed_2P
        12.9%
        44%
        112bp
        16.9M
        CR1332_17111FL-61-01-53_S147_L006_R1_001
        13.1%
        50%
        151bp
        12.2M
        CR1332_17111FL-61-01-53_S147_L006_R2_001
        13.2%
        47%
        151bp
        12.2M
        CR1332_17111FL-61-01-53_S147_L006_trimmed_1P
        12.6%
        46%
        122bp
        12.1M
        CR1332_17111FL-61-01-53_S147_L006_trimmed_2P
        12.7%
        46%
        122bp
        12.1M
        CR1333_17111FL-61-01-54_S148_L006_R1_001
        16.1%
        50%
        151bp
        17.5M
        CR1333_17111FL-61-01-54_S148_L006_R2_001
        16.3%
        47%
        151bp
        17.5M
        CR1333_17111FL-61-01-54_S148_L006_trimmed_1P
        15.4%
        46%
        122bp
        17.3M
        CR1333_17111FL-61-01-54_S148_L006_trimmed_2P
        15.7%
        46%
        122bp
        17.3M
        CR1334_17111FL-61-01-55_S149_L006_R1_001
        15.9%
        49%
        151bp
        14.8M
        CR1334_17111FL-61-01-55_S149_L006_R2_001
        16.0%
        48%
        151bp
        14.8M
        CR1334_17111FL-61-01-55_S149_L006_trimmed_1P
        15.3%
        46%
        127bp
        14.6M
        CR1334_17111FL-61-01-55_S149_L006_trimmed_2P
        15.5%
        46%
        127bp
        14.6M
        CR1335_17111FL-61-01-56_S150_L006_R1_001
        14.5%
        48%
        151bp
        14.7M
        CR1335_17111FL-61-01-56_S150_L006_R2_001
        14.7%
        47%
        151bp
        14.7M
        CR1335_17111FL-61-01-56_S150_L006_trimmed_1P
        13.8%
        45%
        122bp
        14.5M
        CR1335_17111FL-61-01-56_S150_L006_trimmed_2P
        14.0%
        45%
        122bp
        14.5M
        CR1336_17111FL-61-01-57_S151_L006_R1_001
        13.9%
        51%
        151bp
        20.0M
        CR1336_17111FL-61-01-57_S151_L006_R2_001
        14.2%
        50%
        151bp
        20.0M
        CR1336_17111FL-61-01-57_S151_L006_trimmed_1P
        13.0%
        49%
        151bp
        19.8M
        CR1336_17111FL-61-01-57_S151_L006_trimmed_2P
        13.4%
        49%
        151bp
        19.8M
        CR1337_17111FL-61-01-58_S152_L006_R1_001
        26.3%
        48%
        151bp
        16.4M
        CR1337_17111FL-61-01-58_S152_L006_R2_001
        26.5%
        47%
        151bp
        16.4M
        CR1337_17111FL-61-01-58_S152_L006_trimmed_1P
        24.7%
        46%
        151bp
        16.2M
        CR1337_17111FL-61-01-58_S152_L006_trimmed_2P
        25.0%
        46%
        151bp
        16.2M
        CR1338_17111FL-61-01-59_S153_L006_R1_001
        42.9%
        48%
        151bp
        16.3M
        CR1338_17111FL-61-01-59_S153_L006_R2_001
        43.1%
        47%
        151bp
        16.3M
        CR1338_17111FL-61-01-59_S153_L006_trimmed_1P
        41.3%
        46%
        151bp
        16.1M
        CR1338_17111FL-61-01-59_S153_L006_trimmed_2P
        41.7%
        46%
        151bp
        16.1M
        CR1339_17111FL-61-01-60_S154_L006_R1_001
        28.2%
        47%
        151bp
        13.7M
        CR1339_17111FL-61-01-60_S154_L006_R2_001
        28.5%
        47%
        151bp
        13.7M
        CR1339_17111FL-61-01-60_S154_L006_trimmed_1P
        26.6%
        45%
        151bp
        13.5M
        CR1339_17111FL-61-01-60_S154_L006_trimmed_2P
        27.1%
        46%
        151bp
        13.5M
        CR1340_17111FL-61-01-61_S155_L006_R1_001
        18.5%
        47%
        151bp
        14.7M
        CR1340_17111FL-61-01-61_S155_L006_R2_001
        19.0%
        46%
        151bp
        14.7M
        CR1340_17111FL-61-01-61_S155_L006_trimmed_1P
        17.8%
        45%
        151bp
        14.6M
        CR1340_17111FL-61-01-61_S155_L006_trimmed_2P
        18.2%
        45%
        151bp
        14.6M
        CR1341_17111FL-61-01-62_S156_L006_R1_001
        26.4%
        48%
        151bp
        17.3M
        CR1341_17111FL-61-01-62_S156_L006_R2_001
        26.8%
        46%
        151bp
        17.3M
        CR1341_17111FL-61-01-62_S156_L006_trimmed_1P
        24.9%
        45%
        151bp
        17.1M
        CR1341_17111FL-61-01-62_S156_L006_trimmed_2P
        25.3%
        45%
        151bp
        17.1M
        CR1342_17111FL-61-01-63_S157_L006_R1_001
        31.5%
        48%
        151bp
        15.3M
        CR1342_17111FL-61-01-63_S157_L006_R2_001
        31.6%
        47%
        151bp
        15.3M
        CR1342_17111FL-61-01-63_S157_L006_trimmed_1P
        30.0%
        46%
        151bp
        15.1M
        CR1342_17111FL-61-01-63_S157_L006_trimmed_2P
        30.3%
        46%
        151bp
        15.1M
        CR1343_17111FL-61-01-64_S158_L006_R1_001
        31.4%
        49%
        151bp
        17.2M
        CR1343_17111FL-61-01-64_S158_L006_R2_001
        31.6%
        48%
        151bp
        17.2M
        CR1343_17111FL-61-01-64_S158_L006_trimmed_1P
        29.6%
        47%
        151bp
        17.0M
        CR1343_17111FL-61-01-64_S158_L006_trimmed_2P
        29.9%
        47%
        151bp
        17.0M
        CR1344_17111FL-61-01-65_S159_L006_R1_001
        12.7%
        52%
        151bp
        15.8M
        CR1344_17111FL-61-01-65_S159_L006_R2_001
        12.8%
        51%
        151bp
        15.8M
        CR1344_17111FL-61-01-65_S159_L006_trimmed_1P
        12.0%
        50%
        151bp
        15.7M
        CR1344_17111FL-61-01-65_S159_L006_trimmed_2P
        12.2%
        50%
        151bp
        15.7M
        CR1345_17111FL-61-01-66_S160_L006_R1_001
        26.4%
        49%
        151bp
        17.3M
        CR1345_17111FL-61-01-66_S160_L006_R2_001
        26.6%
        48%
        151bp
        17.3M
        CR1345_17111FL-61-01-66_S160_L006_trimmed_1P
        24.9%
        46%
        151bp
        17.1M
        CR1345_17111FL-61-01-66_S160_L006_trimmed_2P
        25.2%
        46%
        151bp
        17.1M
        CR1346_17111FL-61-01-67_S161_L006_R1_001
        31.0%
        48%
        151bp
        14.5M
        CR1346_17111FL-61-01-67_S161_L006_R2_001
        31.4%
        47%
        151bp
        14.5M
        CR1346_17111FL-61-01-67_S161_L006_trimmed_1P
        29.6%
        46%
        151bp
        14.3M
        CR1346_17111FL-61-01-67_S161_L006_trimmed_2P
        30.1%
        46%
        151bp
        14.3M
        CR1347_17111FL-61-01-68_S162_L006_R1_001
        27.6%
        49%
        151bp
        17.0M
        CR1347_17111FL-61-01-68_S162_L006_R2_001
        28.0%
        47%
        151bp
        17.0M
        CR1347_17111FL-61-01-68_S162_L006_trimmed_1P
        26.2%
        46%
        151bp
        16.8M
        CR1347_17111FL-61-01-68_S162_L006_trimmed_2P
        26.7%
        46%
        151bp
        16.8M
        CR1348_17111FL-61-01-69_S163_L006_R1_001
        21.6%
        49%
        151bp
        15.3M
        CR1348_17111FL-61-01-69_S163_L006_R2_001
        22.0%
        48%
        151bp
        15.3M
        CR1348_17111FL-61-01-69_S163_L006_trimmed_1P
        20.3%
        46%
        151bp
        15.2M
        CR1348_17111FL-61-01-69_S163_L006_trimmed_2P
        20.7%
        46%
        151bp
        15.2M
        CR1349_17111FL-61-01-70_S164_L006_R1_001
        22.8%
        50%
        151bp
        13.9M
        CR1349_17111FL-61-01-70_S164_L006_R2_001
        23.2%
        48%
        151bp
        13.9M
        CR1349_17111FL-61-01-70_S164_L006_trimmed_1P
        21.4%
        47%
        151bp
        13.7M
        CR1349_17111FL-61-01-70_S164_L006_trimmed_2P
        21.9%
        47%
        151bp
        13.7M
        CR1350_17111FL-61-01-71_S165_L006_R1_001
        27.4%
        50%
        151bp
        15.8M
        CR1350_17111FL-61-01-71_S165_L006_R2_001
        27.9%
        48%
        151bp
        15.8M
        CR1350_17111FL-61-01-71_S165_L006_trimmed_1P
        26.0%
        47%
        151bp
        15.6M
        CR1350_17111FL-61-01-71_S165_L006_trimmed_2P
        26.6%
        47%
        151bp
        15.6M
        CR1351_17111FL-61-01-72_S166_L006_R1_001
        29.0%
        50%
        151bp
        15.2M
        CR1351_17111FL-61-01-72_S166_L006_R2_001
        29.2%
        48%
        151bp
        15.2M
        CR1351_17111FL-61-01-72_S166_L006_trimmed_1P
        27.2%
        47%
        151bp
        15.1M
        CR1351_17111FL-61-01-72_S166_L006_trimmed_2P
        27.6%
        47%
        151bp
        15.1M
        CR1352_17111FL-61-01-73_S167_L006_R1_001
        13.3%
        50%
        151bp
        19.3M
        CR1352_17111FL-61-01-73_S167_L006_R2_001
        13.7%
        49%
        151bp
        19.3M
        CR1352_17111FL-61-01-73_S167_L006_trimmed_1P
        12.2%
        48%
        151bp
        19.1M
        CR1352_17111FL-61-01-73_S167_L006_trimmed_2P
        12.7%
        48%
        151bp
        19.1M
        CR1353_17111FL-61-01-74_S168_L006_R1_001
        24.1%
        49%
        151bp
        15.0M
        CR1353_17111FL-61-01-74_S168_L006_R2_001
        24.1%
        47%
        151bp
        15.0M
        CR1353_17111FL-61-01-74_S168_L006_trimmed_1P
        22.4%
        46%
        151bp
        14.8M
        CR1353_17111FL-61-01-74_S168_L006_trimmed_2P
        22.6%
        46%
        151bp
        14.8M
        CR1354_17111FL-61-01-75_S169_L006_R1_001
        37.2%
        50%
        151bp
        15.4M
        CR1354_17111FL-61-01-75_S169_L006_R2_001
        37.4%
        48%
        151bp
        15.4M
        CR1354_17111FL-61-01-75_S169_L006_trimmed_1P
        35.2%
        46%
        142bp
        15.2M
        CR1354_17111FL-61-01-75_S169_L006_trimmed_2P
        35.7%
        46%
        142bp
        15.2M
        CR1355_17111FL-61-01-76_S170_L006_R1_001
        26.7%
        47%
        151bp
        16.6M
        CR1355_17111FL-61-01-76_S170_L006_R2_001
        26.9%
        47%
        151bp
        16.6M
        CR1355_17111FL-61-01-76_S170_L006_trimmed_1P
        24.8%
        45%
        151bp
        16.4M
        CR1355_17111FL-61-01-76_S170_L006_trimmed_2P
        25.1%
        45%
        151bp
        16.4M
        CR1356_17111FL-61-01-77_S171_L006_R1_001
        25.8%
        47%
        151bp
        14.8M
        CR1356_17111FL-61-01-77_S171_L006_R2_001
        26.1%
        46%
        151bp
        14.8M
        CR1356_17111FL-61-01-77_S171_L006_trimmed_1P
        24.9%
        45%
        151bp
        14.6M
        CR1356_17111FL-61-01-77_S171_L006_trimmed_2P
        25.2%
        45%
        151bp
        14.6M
        CR1357_17111FL-61-01-78_S172_L006_R1_001
        26.1%
        46%
        151bp
        15.9M
        CR1357_17111FL-61-01-78_S172_L006_R2_001
        26.4%
        46%
        151bp
        15.9M
        CR1357_17111FL-61-01-78_S172_L006_trimmed_1P
        24.8%
        44%
        151bp
        15.7M
        CR1357_17111FL-61-01-78_S172_L006_trimmed_2P
        25.2%
        44%
        151bp
        15.7M
        CR1358_17111FL-61-01-79_S173_L006_R1_001
        29.9%
        49%
        151bp
        14.7M
        CR1358_17111FL-61-01-79_S173_L006_R2_001
        30.2%
        48%
        151bp
        14.7M
        CR1358_17111FL-61-01-79_S173_L006_trimmed_1P
        28.1%
        47%
        151bp
        14.5M
        CR1358_17111FL-61-01-79_S173_L006_trimmed_2P
        28.5%
        47%
        151bp
        14.5M
        CR1359_17111FL-61-01-80_S174_L006_R1_001
        32.5%
        49%
        151bp
        14.2M
        CR1359_17111FL-61-01-80_S174_L006_R2_001
        32.8%
        47%
        151bp
        14.2M
        CR1359_17111FL-61-01-80_S174_L006_trimmed_1P
        30.5%
        46%
        151bp
        14.0M
        CR1359_17111FL-61-01-80_S174_L006_trimmed_2P
        30.9%
        46%
        151bp
        14.0M
        CR1360_17111FL-61-01-81_S175_L006_R1_001
        12.7%
        51%
        151bp
        17.4M
        CR1360_17111FL-61-01-81_S175_L006_R2_001
        12.8%
        50%
        151bp
        17.4M
        CR1360_17111FL-61-01-81_S175_L006_trimmed_1P
        12.0%
        49%
        151bp
        17.2M
        CR1360_17111FL-61-01-81_S175_L006_trimmed_2P
        12.2%
        49%
        151bp
        17.2M
        CR1361_17111FL-61-01-82_S176_L006_R1_001
        23.0%
        49%
        151bp
        14.4M
        CR1361_17111FL-61-01-82_S176_L006_R2_001
        23.3%
        47%
        151bp
        14.4M
        CR1361_17111FL-61-01-82_S176_L006_trimmed_1P
        21.4%
        46%
        151bp
        14.2M
        CR1361_17111FL-61-01-82_S176_L006_trimmed_2P
        21.9%
        46%
        151bp
        14.2M
        CR1362_17111FL-61-01-83_S177_L006_R1_001
        34.9%
        50%
        151bp
        18.4M
        CR1362_17111FL-61-01-83_S177_L006_R2_001
        35.1%
        49%
        151bp
        18.4M
        CR1362_17111FL-61-01-83_S177_L006_trimmed_1P
        33.1%
        47%
        147bp
        18.2M
        CR1362_17111FL-61-01-83_S177_L006_trimmed_2P
        33.3%
        47%
        147bp
        18.2M
        CR1363_17111FL-61-01-84_S178_L006_R1_001
        26.8%
        48%
        151bp
        15.9M
        CR1363_17111FL-61-01-84_S178_L006_R2_001
        27.0%
        47%
        151bp
        15.9M
        CR1363_17111FL-61-01-84_S178_L006_trimmed_1P
        25.2%
        46%
        151bp
        15.7M
        CR1363_17111FL-61-01-84_S178_L006_trimmed_2P
        25.5%
        46%
        151bp
        15.7M
        CR1364_17111FL-61-01-85_S179_L006_R1_001
        14.5%
        46%
        151bp
        15.9M
        CR1364_17111FL-61-01-85_S179_L006_R2_001
        14.9%
        46%
        151bp
        15.9M
        CR1364_17111FL-61-01-85_S179_L006_trimmed_1P
        13.8%
        45%
        151bp
        15.7M
        CR1364_17111FL-61-01-85_S179_L006_trimmed_2P
        14.2%
        45%
        151bp
        15.7M
        CR1365_17111FL-61-01-86_S180_L006_R1_001
        20.1%
        48%
        151bp
        16.3M
        CR1365_17111FL-61-01-86_S180_L006_R2_001
        20.5%
        47%
        151bp
        16.3M
        CR1365_17111FL-61-01-86_S180_L006_trimmed_1P
        19.0%
        45%
        151bp
        16.1M
        CR1365_17111FL-61-01-86_S180_L006_trimmed_2P
        19.5%
        45%
        151bp
        16.1M
        CR1366_17111FL-61-01-87_S181_L006_R1_001
        29.4%
        47%
        151bp
        15.6M
        CR1366_17111FL-61-01-87_S181_L006_R2_001
        29.8%
        47%
        151bp
        15.6M
        CR1366_17111FL-61-01-87_S181_L006_trimmed_1P
        28.3%
        46%
        151bp
        15.4M
        CR1366_17111FL-61-01-87_S181_L006_trimmed_2P
        28.8%
        46%
        151bp
        15.4M
        CR1367_17111FL-61-01-88_S182_L006_R1_001
        29.7%
        50%
        151bp
        16.9M
        CR1367_17111FL-61-01-88_S182_L006_R2_001
        29.9%
        49%
        151bp
        16.9M
        CR1367_17111FL-61-01-88_S182_L006_trimmed_1P
        27.9%
        47%
        151bp
        16.7M
        CR1367_17111FL-61-01-88_S182_L006_trimmed_2P
        28.2%
        47%
        151bp
        16.7M

        FastQC

        Version: 0.11.9

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        127
        4764696
        0.1210%
        ATACGCGGCCGCCGAAACGCGTATCGCGCGCATAATAGCTCAATTGGTCG
        86
        2433279
        0.0618%
        CAAGGTCGCTGTTCAATACATCGGATATCGCGCGAAACGACCGTTCGGCC
        67
        2086771
        0.0530%
        GATAGACAGCTGCTGAACCAATGGGACCAAGCTTCACACCGAGTTCATCG
        64
        3473186
        0.0882%
        CAAGGTCGCTGTTCAATACATCGGAGTGATATCGCGTTAACGTCGCGGCC
        53
        1333070
        0.0338%
        AGACAGCTGCTGAACCAATGGGACCAAGCTTCACACCGAGTTCATCGCTT
        37
        1290506
        0.0328%
        ACGCGGCCGCCGAAACGCGTATCGCGCGCATAATAGCTCAATTGGTCGTA
        32
        737588
        0.0187%
        CAAGGTCGCTGTTCAATACATCGGACCGCGATACGACTCGTTCGTCGGCC
        32
        1678107
        0.0426%
        CAAGGTCGCTGTTCAATACATCGGACCGCGCGTAATGCGCGACGTTAGCC
        32
        1460982
        0.0371%
        ATGTGTTCGACCCTATACGCGGCCGCCGAAACGCGTATCGCGCGCATAAT
        17
        341383
        0.0087%
        TACGCGGCCGCCGAAACGCGTATCGCGCGCATAATAGCTCAATTGGTCGT
        15
        262366
        0.0067%
        GCTGAACCAATGGGACCAAGCTTCACACCGAGTTCATCGCTTATGTGTTC
        10
        221406
        0.0056%
        CAAGGTCGCTGTTCAATACATCGGACGACGTTAACGCGTTTCGTACGGCC
        4
        58190
        0.0015%
        GAACCAATGGGACCAAGCTTCACACCGAGTTCATCGCTTATGTGTTCGAC
        4
        51756
        0.0013%
        ATGGGACCAAGCTTCACACCGAGTTCATCGCTTATGTGTTCGACCCTATA
        4
        94748
        0.0024%
        TGTGTTCGACCCTATACGCGGCCGCCGAAACGCGTATCGCGCGCATAATA
        4
        85664
        0.0022%
        ACAGCTGCTGAACCAATGGGACCAAGCTTCACACCGAGTTCATCGCTTAT
        4
        65286
        0.0017%
        CAAGGTCGCTGTTCAATACATCGGACGCGACTATCGCGCGTAACGCGGCC
        2
        26233
        0.0007%
        CAAGGTCGCTGTTCAATACATCGGATCGACGCGTAAACGGTACGTCGGCC
        2
        25199
        0.0006%
        CGCGGCCGCCGAAACGCGTATCGCGCGCATAATAGCTCAATTGGTCGTAG
        2
        30539
        0.0008%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        FastQ Screen

        Version: 0.14.0

        FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.DOI: 10.12688/f1000research.15931.2.

        Mapped Reads

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQ Screen0.14.0
        FastQC0.11.9

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.