BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 9,803,276 number of mapped reads = 9,541,517 (97.33%) number of supplementary alignments = 953,854 (9.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,781,052 number of mapped paired reads (second in pair) = 4,760,465 number of mapped paired reads (both in pair) = 9,365,138 number of mapped paired reads (singletons) = 176,379 number of mapped bases = 1,126,309,856 bp number of sequenced bases = 1,125,688,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,335,410 duplication rate = 64.75% >>>>>>> Insert size mean insert size = 815,473.8065 std insert size = 8,183,374.7669 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.7249 >>>>>>> ACTG content number of A's = 340,907,340 bp (30.28%) number of C's = 218,048,197 bp (19.37%) number of T's = 340,488,859 bp (30.25%) number of G's = 226,230,434 bp (20.1%) number of N's = 13,805 bp (0%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 11,401,377 number of insertions = 115,655 mapped reads with insertion percentage = 1.17% number of deletions = 250,636 mapped reads with deletion percentage = 2.56% homopolymer indels = 43.22% >>>>>>> Coverage mean coverageData = 0.3638X std coverageData = 5.1185X There is a 7.55% of reference with a coverageData >= 1X There is a 5.97% of reference with a coverageData >= 2X There is a 4.59% of reference with a coverageData >= 3X There is a 3.75% of reference with a coverageData >= 4X There is a 2.85% of reference with a coverageData >= 5X There is a 2.3% of reference with a coverageData >= 6X There is a 1.71% of reference with a coverageData >= 7X There is a 1.39% of reference with a coverageData >= 8X There is a 1.04% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 99134456 0.397730026116966 2.6753360907700263 chr2 243199373 82521953 0.33931811575846454 15.638238332741727 chr3 198022430 71150729 0.359306412914941 1.7041920108797581 chr4 191154276 69734971 0.3648098931357413 2.4748767946893144 chr5 180915260 56077336 0.3099646541701347 1.5612168960926855 chr6 171115067 53816073 0.314502246608126 1.7214249754582907 chr7 159138663 97521227 0.6128066251254103 5.180767494816698 chr8 146364022 120837643 0.8255966278379533 3.877732253800134 chr9 141213431 38768734 0.27453999046308847 2.195945197949216 chr10 135534747 49881867 0.3680374819307406 5.982816316883711 chr11 135006516 45531588 0.3372547440599089 1.739000359285651 chr12 133851895 42088910 0.3144438859083766 1.6051221802090387 chr13 115169878 33860039 0.29400082372232783 1.5380937175354128 chr14 107349540 38995703 0.3632591532297204 1.739961247662121 chr15 102531392 26172920 0.25526738191557957 1.4242902671732431 chr16 90354753 24868630 0.27523322431084507 2.3933540709657675 chr17 81195210 29538688 0.36379840633456084 2.0712146766201216 chr18 78077248 19430574 0.24886345891699463 2.942091705380763 chr19 59128983 14172880 0.23969429678842946 2.1702253311367787 chr20 63025520 41495390 0.6583902838088445 2.369721885150079 chr21 48129895 13016563 0.27044652808820796 1.776560008208301 chr22 51304566 11068046 0.21573218258975235 1.2581767159148125 chrMT 16571 2741142 165.41801943153703 109.4946292171545 chrX 155270560 41755682 0.2689220802707223 1.489022784753597 chrY 59373566 2128112 0.03584275197484348 1.4413251230740973