BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618627.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 37,472,144 number of mapped reads = 36,179,437 (96.55%) number of supplementary alignments = 120,945 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,271,117 number of mapped paired reads (second in pair) = 17,908,320 number of mapped paired reads (both in pair) = 35,571,384 number of mapped paired reads (singletons) = 608,053 number of mapped bases = 3,384,135,349 bp number of sequenced bases = 3,381,745,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,597,654 duplication rate = 34.49% >>>>>>> Insert size mean insert size = 73,796.7084 std insert size = 2,727,471.1663 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.1906 >>>>>>> ACTG content number of A's = 929,376,194 bp (27.48%) number of C's = 720,926,157 bp (21.32%) number of T's = 945,594,682 bp (27.96%) number of G's = 785,728,143 bp (23.23%) number of N's = 120,011 bp (0%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 40,145,876 number of insertions = 614,627 mapped reads with insertion percentage = 1.67% number of deletions = 1,753,704 mapped reads with deletion percentage = 4.72% homopolymer indels = 53.04% >>>>>>> Coverage mean coverageData = 1.0932X std coverageData = 4.3773X There is a 20.47% of reference with a coverageData >= 1X There is a 14.46% of reference with a coverageData >= 2X There is a 10.86% of reference with a coverageData >= 3X There is a 8.73% of reference with a coverageData >= 4X There is a 7.09% of reference with a coverageData >= 5X There is a 5.93% of reference with a coverageData >= 6X There is a 4.97% of reference with a coverageData >= 7X There is a 4.24% of reference with a coverageData >= 8X There is a 3.63% of reference with a coverageData >= 9X There is a 3.14% of reference with a coverageData >= 10X There is a 2.72% of reference with a coverageData >= 11X There is a 2.37% of reference with a coverageData >= 12X There is a 2.07% of reference with a coverageData >= 13X There is a 1.82% of reference with a coverageData >= 14X There is a 1.61% of reference with a coverageData >= 15X There is a 1.42% of reference with a coverageData >= 16X There is a 1.26% of reference with a coverageData >= 17X There is a 1.12% of reference with a coverageData >= 18X There is a 1% of reference with a coverageData >= 19X There is a 0.89% of reference with a coverageData >= 20X There is a 0.8% of reference with a coverageData >= 21X There is a 0.72% of reference with a coverageData >= 22X There is a 0.64% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.52% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 295219095 1.184426718038147 5.497273872694104 chr2 243199373 304686202 1.2528247842152125 5.088605050049095 chr3 198022430 226298425 1.1427918796875687 3.8102785272202366 chr4 191154276 179299600 0.9379837257734166 3.6402266133589696 chr5 180915260 202708324 1.1204600651155685 3.7686566067122342 chr6 171115067 188095798 1.0992357440972746 3.7757404087754134 chr7 159138663 172799997 1.085845474270448 3.7528433287998437 chr8 146364022 196377769 1.3417079301086712 4.322677796052894 chr9 141213431 151535536 1.0730957737299083 4.639894432425251 chr10 135534747 180618499 1.3326361172902768 4.42276779652624 chr11 135006516 185065724 1.370791051300072 5.054116969284024 chr12 133851895 160279256 1.1974373317613471 4.1948821323381456 chr13 115169878 92654105 0.804499462958535 3.075895868815076 chr14 107349540 96962809 0.9032438238673403 3.634114170768453 chr15 102531392 109335776 1.0663639093088682 3.8328982971926795 chr16 90354753 115643608 1.2798840587832718 7.2124877592321806 chr17 81195210 126025055 1.5521242570836382 5.110231489174239 chr18 78077248 91248691 1.168697582681193 4.490283621173989 chr19 59128983 72887018 1.2326783635023792 5.010850276333713 chr20 63025520 98194490 1.558011580071057 4.760474965827093 chr21 48129895 44050774 0.9152476646790939 5.230627693553443 chr22 51304566 52429317 1.0219230194832951 3.9299799880683643 chrMT 16571 639524 38.59296361112787 37.00273913263587 chrX 155270560 9646020 0.062123946741739065 1.0995377343213555 chrY 59373566 31433937 0.5294264622744741 3.3279407471856435