BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084859.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,400,888 number of mapped reads = 2,130,830 (88.75%) number of supplementary alignments = 14,608 (0.61%) number of secondary alignments = 0 number of mapped bases = 145,378,033 bp number of sequenced bases = 145,317,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,894 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6224 >>>>>>> ACTG content number of A's = 41,524,968 bp (28.58%) number of C's = 26,513,681 bp (18.25%) number of T's = 46,554,093 bp (32.04%) number of G's = 30,702,839 bp (21.13%) number of N's = 22,131 bp (0.02%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,239,216 number of insertions = 11,662 mapped reads with insertion percentage = 0.54% number of deletions = 34,136 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.047X std coverageData = 0.4337X There is a 3.98% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% 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 11867285 0.04761185730405863 0.8031899416359549 chr2 243199373 12852735 0.052848553190965666 0.4024959494570522 chr3 198022430 9661961 0.048792255503581086 0.25126165174457665 chr4 191154276 9671059 0.05059295142317402 0.2749931155554697 chr5 180915260 9186473 0.05077776744758845 0.258578213635546 chr6 171115067 8843659 0.05168252658896484 0.2729351714170726 chr7 159138663 8148819 0.05120577769338178 0.45416774128054205 chr8 146364022 7742736 0.05290054136391524 0.86544248864053 chr9 141213431 5977434 0.04232907562454169 0.37947354229608243 chr10 135534747 6754154 0.04983337593864399 0.39570748609300593 chr11 135006516 6671492 0.04941607411008221 0.35233361858820345 chr12 133851895 6706197 0.050101621646820915 0.2589177193650162 chr13 115169878 4769948 0.041416628052692736 0.23107972117428976 chr14 107349540 4489742 0.04182357930923598 0.2514988437329422 chr15 102531392 4124955 0.04023114208768374 0.22698878164725325 chr16 90354753 3881583 0.04295936706284837 0.2651630119533318 chr17 81195210 3540192 0.04360099567449853 0.28206183086510256 chr18 78077248 3970334 0.05085135685110213 0.7908235635329602 chr19 59128983 2475238 0.04186167044341013 0.5619109684624063 chr20 63025520 2898491 0.04598916438928231 0.26057809173933383 chr21 48129895 1851355 0.038465801764163414 0.24217047528601496 chr22 51304566 1387224 0.02703899687992683 0.18435254089369094 chrMT 16571 36608 2.209160581739183 1.9359898789817167 chrX 155270560 7523991 0.04845729286994264 0.275616330910185 chrY 59373566 344368 0.005800022184956855 0.14142810530534458