BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089710.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,012,166 number of mapped reads = 14,769,916 (82%) number of supplementary alignments = 593 (0%) number of secondary alignments = 0 number of mapped bases = 698,541,350 bp number of sequenced bases = 698,396,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,157,654 duplication rate = 12.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6144 >>>>>>> ACTG content number of A's = 202,940,511 bp (29.06%) number of C's = 142,176,574 bp (20.36%) number of T's = 205,159,376 bp (29.38%) number of G's = 148,087,453 bp (21.2%) number of N's = 32,684 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 3,621,853 number of insertions = 33,350 mapped reads with insertion percentage = 0.23% number of deletions = 93,918 mapped reads with deletion percentage = 0.63% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.2256X std coverageData = 1.5684X There is a 9.19% of reference with a coverageData >= 1X There is a 4.91% of reference with a coverageData >= 2X There is a 2.93% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 56288860 0.2258323761608602 2.733041163375706 chr2 243199373 59055502 0.24282752571076735 1.5376795666322125 chr3 198022430 47122958 0.23796777971061156 0.9905017868055274 chr4 191154276 44850817 0.234631513029821 1.1277792311819317 chr5 180915260 43020504 0.2377936720208124 0.999663575232731 chr6 171115067 40827768 0.2385983228466959 1.1006467899355374 chr7 159138663 38283025 0.24056394768127468 2.1656519829964647 chr8 146364022 35344316 0.24148226809454582 2.158666030332041 chr9 141213431 28997878 0.20534787516068495 1.3800267078900348 chr10 135534747 32691521 0.24120398439228283 1.5477098071570583 chr11 135006516 32083469 0.23764385564915994 1.462378721830421 chr12 133851895 31326429 0.23403799400822828 1.0551764991922596 chr13 115169878 21786639 0.18916959345915083 0.8826043892060275 chr14 107349540 21376621 0.19913099767358108 0.9802892894727078 chr15 102531392 20560406 0.20052791246606697 0.9098101031233436 chr16 90354753 19327879 0.21391103797273398 1.0464298675369967 chr17 81195210 19048724 0.23460403637111105 1.156436385186648 chr18 78077248 18037545 0.23102178242757737 2.9940963221306975 chr19 59128983 14036122 0.23738142088457703 1.964949543812385 chr20 63025520 14496051 0.23000287819918028 1.0885331643487857 chr21 48129895 9131352 0.18972308167304333 1.1136931436275734 chr22 51304566 8086492 0.1576173941321324 0.8010808032599445 chrMT 16571 400208 24.15110735622473 15.987958460122192 chrX 155270560 39993417 0.25757244000408064 1.2151354953937965 chrY 59373566 2366847 0.0398636490858575 1.0549427086896817