BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163162.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 = 36,641,548 number of mapped reads = 36,075,286 (98.45%) number of supplementary alignments = 412,573 (1.13%) number of secondary alignments = 0 number of mapped bases = 3,587,251,151 bp number of sequenced bases = 3,586,614,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,835,199 duplication rate = 40.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.5263 >>>>>>> ACTG content number of A's = 943,071,095 bp (26.29%) number of C's = 850,682,350 bp (23.72%) number of T's = 955,640,970 bp (26.64%) number of G's = 834,572,581 bp (23.27%) number of N's = 2,647,330 bp (0.07%) GC percentage = 46.99% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 27,577,431 number of insertions = 268,121 mapped reads with insertion percentage = 0.73% number of deletions = 314,438 mapped reads with deletion percentage = 0.86% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 1.1588X std coverageData = 11.2722X There is a 6.58% of reference with a coverageData >= 1X There is a 4.85% of reference with a coverageData >= 2X There is a 4.02% of reference with a coverageData >= 3X There is a 3.59% of reference with a coverageData >= 4X There is a 3.26% of reference with a coverageData >= 5X There is a 3.02% of reference with a coverageData >= 6X There is a 2.82% of reference with a coverageData >= 7X There is a 2.64% of reference with a coverageData >= 8X There is a 2.49% of reference with a coverageData >= 9X There is a 2.36% of reference with a coverageData >= 10X There is a 2.24% of reference with a coverageData >= 11X There is a 2.14% of reference with a coverageData >= 12X There is a 2.04% of reference with a coverageData >= 13X There is a 1.95% of reference with a coverageData >= 14X There is a 1.86% of reference with a coverageData >= 15X There is a 1.78% of reference with a coverageData >= 16X There is a 1.71% of reference with a coverageData >= 17X There is a 1.64% of reference with a coverageData >= 18X There is a 1.58% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.46% of reference with a coverageData >= 21X There is a 1.41% of reference with a coverageData >= 22X There is a 1.36% of reference with a coverageData >= 23X There is a 1.31% of reference with a coverageData >= 24X There is a 1.26% of reference with a coverageData >= 25X There is a 1.22% of reference with a coverageData >= 26X There is a 1.18% of reference with a coverageData >= 27X There is a 1.14% of reference with a coverageData >= 28X There is a 1.1% of reference with a coverageData >= 29X There is a 1.07% of reference with a coverageData >= 30X There is a 1.04% of reference with a coverageData >= 31X There is a 1% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.91% of reference with a coverageData >= 35X There is a 0.89% of reference with a coverageData >= 36X There is a 0.86% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.81% of reference with a coverageData >= 39X There is a 0.79% of reference with a coverageData >= 40X There is a 0.77% of reference with a coverageData >= 41X There is a 0.74% of reference with a coverageData >= 42X There is a 0.72% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 401640114 1.6113906251812307 14.110342412419568 chr2 243199373 244277893 1.004434715380619 9.629324561592238 chr3 198022430 173212673 0.8747123899045174 7.896263416815345 chr4 191154276 138630709 0.7252294424216804 9.583792568346958 chr5 180915260 166101862 0.9181196876371844 11.65078177858519 chr6 171115067 188965837 1.1043202700554708 10.411543987198757 chr7 159138663 203906232 1.2813117073881664 13.533975972213844 chr8 146364022 153822185 1.050956258909037 13.697257436721474 chr9 141213431 145186368 1.0281342714490096 8.930119017482951 chr10 135534747 146478629 1.0807459507044346 9.542108844179635 chr11 135006516 167394496 1.2398993838193706 9.772068425083912 chr12 133851895 174619180 1.3045700996612712 10.305323758966095 chr13 115169878 64995605 0.5643455227069009 6.5643304933335855 chr14 107349540 99270466 0.9247404879424728 8.463708962155845 chr15 102531392 142602074 1.3908137909607234 11.10639136061337 chr16 90354753 140712804 1.5573370445714128 12.608394092869098 chr17 81195210 194548534 2.396059250293213 16.051970356608848 chr18 78077248 57754568 0.7397106004555898 7.958700002108777 chr19 59128983 209512144 3.5433070783578335 20.441119783023023 chr20 63025520 77179979 1.224582978450634 10.487572304344797 chr21 48129895 43136501 0.8962517163189323 11.618602829693984 chr22 51304566 75713903 1.4757731894662163 11.68950161530109 chrMT 16571 19840 1.1972723432502566 1.4235805622319235 chrX 155270560 173706559 1.1187346719172004 13.170702063092325 chrY 59373566 3861996 0.06504571411459437 6.461128151873069