BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548963.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 = 10,524,558 number of mapped reads = 9,009,882 (85.61%) number of secondary alignments = 0 number of mapped bases = 355,957,013 bp number of sequenced bases = 355,923,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 486,506 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.5707 >>>>>>> ACTG content number of A's = 100,175,648 bp (28.15%) number of C's = 76,758,302 bp (21.57%) number of T's = 102,128,894 bp (28.69%) number of G's = 76,859,793 bp (21.59%) number of N's = 515 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,126,822 number of insertions = 12,807 mapped reads with insertion percentage = 0.14% number of deletions = 26,280 mapped reads with deletion percentage = 0.29% homopolymer indels = 37.99% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 1.1974X There is a 9% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 28636654 0.11489100362161184 1.9408401069667636 chr2 243199373 30420579 0.12508494008329538 1.119640270215437 chr3 198022430 23974154 0.12106787094775072 0.43024715518550627 chr4 191154276 23730740 0.12414443713516511 0.5160847367579802 chr5 180915260 22151864 0.12244331406869713 0.4573067652597281 chr6 171115067 20745425 0.12123669390258895 0.4847048506230548 chr7 159138663 20495498 0.12879018595248598 1.727291738032335 chr8 146364022 18503041 0.12641795946274284 2.9787828355377703 chr9 141213431 15377965 0.10889874207503676 1.1830946968228646 chr10 135534747 16878277 0.12453099573056348 0.8785763707929263 chr11 135006516 16501528 0.12222764121992452 0.7618698399876211 chr12 133851895 16398990 0.12251593449610855 0.49498141299734144 chr13 115169878 11218554 0.09740875127088353 0.37110388536085415 chr14 107349540 11044674 0.10288515442171434 0.6391904191765011 chr15 102531392 9931563 0.09686363177435453 0.3918514069072027 chr16 90354753 10072097 0.11147279656666208 0.5769284531376492 chr17 81195210 9651919 0.11887300987336569 0.4702284843568924 chr18 78077248 9531190 0.12207384666016917 2.1677330450530943 chr19 59128983 7961662 0.1346490603432161 1.9638518937114902 chr20 63025520 7170437 0.11377037428647951 0.4802804587211375 chr21 48129895 4580577 0.09517114051464272 0.5970029957663092 chr22 51304566 4104250 0.0799977530265045 0.571140772596684 chrMT 16571 11642 0.7025526522237644 1.051659224928839 chrX 155270560 13454345 0.08665097234144065 0.6098263625329222 chrY 59373566 3409388 0.05742265842681573 0.5299014984272803