BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549001.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 = 9,821,846 number of mapped reads = 8,511,747 (86.66%) number of secondary alignments = 0 number of mapped bases = 337,978,653 bp number of sequenced bases = 337,941,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 755,190 duplication rate = 8.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5235 >>>>>>> ACTG content number of A's = 101,731,586 bp (30.1%) number of C's = 66,738,648 bp (19.75%) number of T's = 101,957,298 bp (30.17%) number of G's = 67,510,257 bp (19.98%) number of N's = 3,405 bp (0%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 966,658 number of insertions = 10,439 mapped reads with insertion percentage = 0.12% number of deletions = 28,940 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.1092X std coverageData = 0.8588X There is a 8.13% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.14% 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% 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 26932857 0.10805532556727311 1.3191235049687902 chr2 243199373 29711289 0.12216844407736199 0.5784657525799592 chr3 198022430 24048437 0.12144299511929027 0.43968737528889296 chr4 191154276 23660407 0.12377649872713284 0.47778951124179103 chr5 180915260 22005936 0.12163670438856292 0.44757813514366557 chr6 171115067 20467065 0.11960995229017442 0.513746593316569 chr7 159138663 19018851 0.11951119006196502 0.874679942296987 chr8 146364022 18000084 0.12298161634284688 2.628236974502024 chr9 141213431 14293005 0.101215620205418 0.5386906984859513 chr10 135534747 16108735 0.11885317497217153 0.6449573036800177 chr11 135006516 15660166 0.11599563090717785 0.5482751835971227 chr12 133851895 15814332 0.11814798737066816 0.4519833249178897 chr13 115169878 11550994 0.1002952699142392 0.3966800478534603 chr14 107349540 10650382 0.09921218106756675 0.48703189939948605 chr15 102531392 9514435 0.09279533628100943 0.3803923248084353 chr16 90354753 8831199 0.09773917482791414 0.42963803302362513 chr17 81195210 8052080 0.09916939681540328 0.4357673785554324 chr18 78077248 9242840 0.1183807093200826 1.0551230518702341 chr19 59128983 5512095 0.093221542470974 0.9664884906642264 chr20 63025520 6704736 0.10638128808774604 0.43770075611401604 chr21 48129895 4408159 0.0915887932022291 0.46241012677842575 chr22 51304566 3330279 0.06491194175582735 0.3539036032635302 chrMT 16571 6345 0.38289783356466117 0.7650413009800681 chrX 155270560 11479468 0.07393203193187427 0.43233662947741786 chrY 59373566 2974477 0.05009766467454557 0.510856310735848