BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153334.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 224,415,324 number of mapped reads = 219,638,547 (97.87%) number of supplementary alignments = 1,612,490 (0.72%) number of secondary alignments = 0 number of mapped bases = 21,651,127,068 bp number of sequenced bases = 21,648,614,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,859,666 duplication rate = 66.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.623 >>>>>>> ACTG content number of A's = 4,771,505,091 bp (22.04%) number of C's = 6,061,976,550 bp (28%) number of T's = 4,806,170,549 bp (22.2%) number of G's = 6,002,569,238 bp (27.73%) number of N's = 6,392,804 bp (0.03%) GC percentage = 55.73% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 86,545,386 number of insertions = 816,982 mapped reads with insertion percentage = 0.37% number of deletions = 922,053 mapped reads with deletion percentage = 0.41% homopolymer indels = 39.55% >>>>>>> Coverage mean coverageData = 6.9939X std coverageData = 94.0284X There is a 11.37% of reference with a coverageData >= 1X There is a 8.45% of reference with a coverageData >= 2X There is a 6.45% of reference with a coverageData >= 3X There is a 5.73% of reference with a coverageData >= 4X There is a 5.09% of reference with a coverageData >= 5X There is a 4.78% of reference with a coverageData >= 6X There is a 4.48% of reference with a coverageData >= 7X There is a 4.29% of reference with a coverageData >= 8X There is a 4.12% of reference with a coverageData >= 9X There is a 3.98% of reference with a coverageData >= 10X There is a 3.86% of reference with a coverageData >= 11X There is a 3.75% of reference with a coverageData >= 12X There is a 3.65% of reference with a coverageData >= 13X There is a 3.57% of reference with a coverageData >= 14X There is a 3.49% of reference with a coverageData >= 15X There is a 3.41% of reference with a coverageData >= 16X There is a 3.34% of reference with a coverageData >= 17X There is a 3.28% of reference with a coverageData >= 18X There is a 3.22% of reference with a coverageData >= 19X There is a 3.16% of reference with a coverageData >= 20X There is a 3.1% of reference with a coverageData >= 21X There is a 3.05% of reference with a coverageData >= 22X There is a 3% of reference with a coverageData >= 23X There is a 2.95% of reference with a coverageData >= 24X There is a 2.91% of reference with a coverageData >= 25X There is a 2.87% of reference with a coverageData >= 26X There is a 2.82% of reference with a coverageData >= 27X There is a 2.78% of reference with a coverageData >= 28X There is a 2.75% of reference with a coverageData >= 29X There is a 2.71% of reference with a coverageData >= 30X There is a 2.67% of reference with a coverageData >= 31X There is a 2.64% of reference with a coverageData >= 32X There is a 2.6% of reference with a coverageData >= 33X There is a 2.57% of reference with a coverageData >= 34X There is a 2.54% of reference with a coverageData >= 35X There is a 2.51% of reference with a coverageData >= 36X There is a 2.48% of reference with a coverageData >= 37X There is a 2.45% of reference with a coverageData >= 38X There is a 2.42% of reference with a coverageData >= 39X There is a 2.39% of reference with a coverageData >= 40X There is a 2.37% of reference with a coverageData >= 41X There is a 2.34% of reference with a coverageData >= 42X There is a 2.32% of reference with a coverageData >= 43X There is a 2.29% of reference with a coverageData >= 44X There is a 2.27% of reference with a coverageData >= 45X There is a 2.24% of reference with a coverageData >= 46X There is a 2.22% of reference with a coverageData >= 47X There is a 2.2% of reference with a coverageData >= 48X There is a 2.18% of reference with a coverageData >= 49X There is a 2.16% of reference with a coverageData >= 50X There is a 2.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2241570888 8.993240935596305 94.909328011262 chr2 243199373 980637543 4.032237134920574 47.649209266363336 chr3 198022430 921231670 4.65215819238255 54.86911611923969 chr4 191154276 420578280 2.2002033582549836 41.787310879456975 chr5 180915260 1198868350 6.626684504115352 162.60259739037951 chr6 171115067 540400404 3.1581111673818882 42.643698833298146 chr7 159138663 1205985853 7.578207773430898 142.8575643073661 chr8 146364022 1075745045 7.349791501356802 109.40328897835519 chr9 141213431 521964052 3.696277672057979 49.48733714222131 chr10 135534747 897473415 6.621721992811187 69.01886759382309 chr11 135006516 1181122631 8.748634258512382 82.6473631177523 chr12 133851895 906804800 6.774687799526484 64.4681840059403 chr13 115169878 126777004 1.1007826542978538 15.836641439963149 chr14 107349540 520632471 4.849880781976337 51.46257427606915 chr15 102531392 1098719740 10.715935076742156 102.34089104575766 chr16 90354753 1486334456 16.449986377584363 135.28319153033394 chr17 81195210 1469380738 18.096889434733896 139.45118203850447 chr18 78077248 128487627 1.6456474874729192 27.376822008100618 chr19 59128983 1961127131 33.16693491920874 189.66724005269342 chr20 63025520 651471214 10.33662576683223 91.86403905033052 chr21 48129895 319448675 6.637219445419525 201.17930381121556 chr22 51304566 849377870 16.555599944067357 144.19492041881577 chrMT 16571 2091 0.1261842978697725 0.45304198036799986 chrX 155270560 929563130 5.986731354610945 63.667332323006185 chrY 59373566 17421990 0.29343007627333684 12.529061966867328