BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548934.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,466,443 number of mapped reads = 5,635,713 (87.15%) number of secondary alignments = 0 number of mapped bases = 222,946,313 bp number of sequenced bases = 222,922,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,729 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2461 >>>>>>> ACTG content number of A's = 65,383,358 bp (29.33%) number of C's = 46,231,548 bp (20.74%) number of T's = 65,451,963 bp (29.36%) number of G's = 45,853,938 bp (20.57%) number of N's = 1,931 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 690,629 number of insertions = 7,599 mapped reads with insertion percentage = 0.13% number of deletions = 18,025 mapped reads with deletion percentage = 0.32% homopolymer indels = 40.04% >>>>>>> Coverage mean coverageData = 0.072X std coverageData = 0.9809X There is a 6.13% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17370037 0.06968904201847505 1.0804068051834568 chr2 243199373 18671691 0.07677524316643694 0.5564979434584817 chr3 198022430 15157990 0.07654683360869777 0.3172343009165515 chr4 191154276 14922730 0.07806642002609453 0.3349972837727887 chr5 180915260 13925514 0.07697257821147868 0.32682310932907527 chr6 171115067 13056505 0.07630248597570896 0.36445813770861907 chr7 159138663 12603182 0.07919622901444133 0.7652078017923836 chr8 146364022 11807048 0.0806690595042544 3.7510475323432524 chr9 141213431 9416552 0.06668311883166411 0.536288731451623 chr10 135534747 10251773 0.07563944469531492 0.5071621106500027 chr11 135006516 10094338 0.07476926521087322 0.5542841463357756 chr12 133851895 10109668 0.07552876259241605 0.33329523832052366 chr13 115169878 7263645 0.06306896495974408 0.27983132878457756 chr14 107349540 6749714 0.06287604026994434 0.35247412818796126 chr15 102531392 6266585 0.061118696213545994 0.2810580056484908 chr16 90354753 5886235 0.06514582580951774 0.3481788803553285 chr17 81195210 5611553 0.06911187248607399 0.32875122419855635 chr18 78077248 5969593 0.07645752319548968 1.044477892345204 chr19 59128983 4391181 0.07426444320884058 1.0200862700324158 chr20 63025520 4247310 0.06739032061933008 0.3209320090255601 chr21 48129895 2815890 0.05850604909900593 0.3291888292399559 chr22 51304566 2331763 0.04544942452100657 0.25536758261579107 chrMT 16571 7832 0.47263291292016174 0.8579073436681802 chrX 155270560 13236247 0.08524634032362606 0.43887314201212074 chrY 59373566 781737 0.013166414831812528 0.1865902179344905