BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163034.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 85,049,774 number of mapped reads = 83,043,957 (97.64%) number of supplementary alignments = 419,435 (0.49%) number of secondary alignments = 0 number of mapped bases = 7,939,619,914 bp number of sequenced bases = 7,938,624,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,571,494 duplication rate = 44.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0336 >>>>>>> ACTG content number of A's = 1,882,542,533 bp (23.71%) number of C's = 2,087,635,907 bp (26.3%) number of T's = 1,864,623,863 bp (23.49%) number of G's = 2,099,887,066 bp (26.45%) number of N's = 3,934,952 bp (0.05%) GC percentage = 52.75% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 41,885,061 number of insertions = 512,774 mapped reads with insertion percentage = 0.61% number of deletions = 440,426 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 2.5647X std coverageData = 33.2995X There is a 10.13% of reference with a coverageData >= 1X There is a 6.79% of reference with a coverageData >= 2X There is a 4.9% of reference with a coverageData >= 3X There is a 4.34% of reference with a coverageData >= 4X There is a 3.89% of reference with a coverageData >= 5X There is a 3.62% of reference with a coverageData >= 6X There is a 3.4% of reference with a coverageData >= 7X There is a 3.22% of reference with a coverageData >= 8X There is a 3.07% of reference with a coverageData >= 9X There is a 2.94% of reference with a coverageData >= 10X There is a 2.82% of reference with a coverageData >= 11X There is a 2.71% of reference with a coverageData >= 12X There is a 2.62% of reference with a coverageData >= 13X There is a 2.53% of reference with a coverageData >= 14X There is a 2.45% of reference with a coverageData >= 15X There is a 2.37% of reference with a coverageData >= 16X There is a 2.3% of reference with a coverageData >= 17X There is a 2.23% of reference with a coverageData >= 18X There is a 2.17% of reference with a coverageData >= 19X There is a 2.11% of reference with a coverageData >= 20X There is a 2.06% of reference with a coverageData >= 21X There is a 2% of reference with a coverageData >= 22X There is a 1.95% of reference with a coverageData >= 23X There is a 1.91% of reference with a coverageData >= 24X There is a 1.86% of reference with a coverageData >= 25X There is a 1.82% of reference with a coverageData >= 26X There is a 1.78% of reference with a coverageData >= 27X There is a 1.74% of reference with a coverageData >= 28X There is a 1.7% of reference with a coverageData >= 29X There is a 1.66% of reference with a coverageData >= 30X There is a 1.63% of reference with a coverageData >= 31X There is a 1.59% of reference with a coverageData >= 32X There is a 1.56% of reference with a coverageData >= 33X There is a 1.53% of reference with a coverageData >= 34X There is a 1.5% of reference with a coverageData >= 35X There is a 1.47% of reference with a coverageData >= 36X There is a 1.44% of reference with a coverageData >= 37X There is a 1.42% of reference with a coverageData >= 38X There is a 1.39% of reference with a coverageData >= 39X There is a 1.36% of reference with a coverageData >= 40X There is a 1.34% of reference with a coverageData >= 41X There is a 1.32% of reference with a coverageData >= 42X There is a 1.29% of reference with a coverageData >= 43X There is a 1.27% of reference with a coverageData >= 44X There is a 1.25% of reference with a coverageData >= 45X There is a 1.23% of reference with a coverageData >= 46X There is a 1.21% of reference with a coverageData >= 47X There is a 1.19% of reference with a coverageData >= 48X There is a 1.17% of reference with a coverageData >= 49X There is a 1.15% of reference with a coverageData >= 50X There is a 1.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1263673986 5.069893029474137 47.04687739103997 chr2 243199373 350709584 1.4420661520373246 18.070929720009758 chr3 198022430 331925373 1.6762008879499155 18.96393724554465 chr4 191154276 165323354 0.8648687199652285 12.559987340903417 chr5 180915260 325531252 1.799357621905416 31.705399399858194 chr6 171115067 462012995 2.700013523648388 29.12979055174582 chr7 159138663 493411957 3.1005159129683024 33.28191836007713 chr8 146364022 486038719 3.3207526847000692 72.59560394546767 chr9 141213431 214121245 1.5162951815822674 18.591315974229868 chr10 135534747 174292062 1.2859585151252764 13.777532900886152 chr11 135006516 482453545 3.5735574792552978 33.12735094880296 chr12 133851895 247456004 1.8487299264608843 19.608533520997476 chr13 115169878 92468212 0.8028853864028579 10.514023858321522 chr14 107349540 240677303 2.24199659355783 22.336913900473075 chr15 102531392 198931441 1.94020033396211 19.139360265239183 chr16 90354753 393881652 4.359279826707069 37.47958779464203 chr17 81195210 277484503 3.4174984337130234 29.244094048500422 chr18 78077248 103327138 1.3233962600731008 15.777326312118577 chr19 59128983 690823218 11.68332656761575 83.04484521364255 chr20 63025520 228647584 3.6278571600837246 33.64839954732077 chr21 48129895 122972386 2.5550104773758595 56.808577188690315 chr22 51304566 132516665 2.5829409608493714 25.65758620141412 chrMT 16571 2997 0.18085812564118037 0.5085099355591699 chrX 155270560 450313549 2.900186287728981 30.877956910709475 chrY 59373566 10623190 0.17892120544014486 9.883764522831859