BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818894.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,463,187 number of mapped reads = 1,442,856 (98.61%) number of supplementary alignments = 21,159 (1.45%) number of secondary alignments = 0 number of mapped bases = 133,533,418 bp number of sequenced bases = 133,446,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,255 duplication rate = 15.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.176 >>>>>>> ACTG content number of A's = 38,806,723 bp (29.08%) number of C's = 28,675,675 bp (21.49%) number of T's = 37,737,243 bp (28.28%) number of G's = 28,224,663 bp (21.15%) number of N's = 2,028 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 807,207 number of insertions = 16,867 mapped reads with insertion percentage = 1.12% number of deletions = 44,066 mapped reads with deletion percentage = 2.98% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.5534X There is a 3.15% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 11790337 0.04730313991875671 0.8511871108753757 chr2 243199373 12453698 0.05120777182266831 0.834902267401643 chr3 198022430 7693600 0.03885216437350052 0.2524217049780166 chr4 191154276 5006763 0.026192262630839604 0.29138735727797516 chr5 180915260 6703165 0.03705140738266081 0.264111461793287 chr6 171115067 6152235 0.0359537889202942 0.2769164172676025 chr7 159138663 11088857 0.06968047104932633 1.1930364210615294 chr8 146364022 14350499 0.09804662924608618 0.5135818585945023 chr9 141213431 4546595 0.032196618747971646 0.4237373623071611 chr10 135534747 5765308 0.04253749040458238 0.681621692658986 chr11 135006516 5458860 0.0404340483832647 0.3233614941406178 chr12 133851895 4768040 0.035621759408038266 0.2444492469089587 chr13 115169878 4039096 0.035070767375476423 0.2397426787247905 chr14 107349540 4304363 0.04009670651592918 0.28412661651842125 chr15 102531392 3412948 0.03328685911140268 0.23235918018054655 chr16 90354753 3086335 0.034157970638246334 0.5788934602836027 chr17 81195210 3507915 0.04320347222453147 0.3463646387070956 chr18 78077248 2238237 0.028666955577122802 0.48696493773895033 chr19 59128983 2521296 0.04264061162695797 0.72288939313009 chr20 63025520 5133640 0.08145335413337328 0.39485562980937533 chr21 48129895 1506445 0.03129956963338482 0.25980235079427416 chr22 51304566 1493585 0.02911212619944977 0.23750676609548665 chrMT 16571 162306 9.794580894333475 6.391110738997651 chrX 155270560 5844923 0.03764347214307722 0.2999175414977119 chrY 59373566 504372 0.008494891480831723 0.6416789987903145