BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818736.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 = 1,190,346 number of mapped reads = 1,159,934 (97.45%) number of supplementary alignments = 9,239 (0.78%) number of secondary alignments = 0 number of mapped bases = 78,816,752 bp number of sequenced bases = 78,783,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 459,782 duplication rate = 35.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6014 >>>>>>> ACTG content number of A's = 22,821,066 bp (28.97%) number of C's = 16,057,249 bp (20.38%) number of T's = 22,393,612 bp (28.42%) number of G's = 17,507,295 bp (22.22%) number of N's = 4,519 bp (0.01%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 388,633 number of insertions = 9,023 mapped reads with insertion percentage = 0.76% number of deletions = 20,529 mapped reads with deletion percentage = 1.75% homopolymer indels = 39.91% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.335X There is a 1.36% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 6632227 0.026608667907792295 0.4146266357979183 chr2 243199373 7022799 0.028876715072781046 0.5214947917069642 chr3 198022430 5435070 0.02744673924060017 0.2730625704383335 chr4 191154276 5265811 0.027547440267566916 0.30617578596208117 chr5 180915260 4972670 0.02748618331035204 0.2832139173586555 chr6 171115067 4756288 0.02779584570422428 0.2955771353586811 chr7 159138663 4105434 0.025797841471120065 0.29895691611697256 chr8 146364022 4109100 0.028074522303028815 0.3091425205310136 chr9 141213431 3368154 0.02385151310430238 0.2901126730570354 chr10 135534747 3802216 0.02805344079035319 0.3635307885995336 chr11 135006516 3446860 0.02553106399694071 0.2898206848667233 chr12 133851895 3612710 0.02699035377870444 0.28283062647234947 chr13 115169878 2524590 0.021920575447687805 0.2460607365991815 chr14 107349540 2418700 0.022531069998064267 0.27717768537204773 chr15 102531392 2298571 0.022418217047126408 0.2507383404321764 chr16 90354753 2292928 0.02537694945610664 0.3740840369811229 chr17 81195210 2118233 0.026088152244448902 0.2800297969469912 chr18 78077248 2127316 0.027246298435108778 0.3792592823297147 chr19 59128983 1456857 0.024638627726778252 0.3718825461054785 chr20 63025520 1685154 0.026737645322085404 0.2833047865226117 chr21 48129895 1075205 0.022339649816397897 0.2561132664463302 chr22 51304566 967990 0.018867521459980774 0.2486293924342282 chrMT 16571 64614 3.8992215315913343 4.596856461672549 chrX 155270560 2534621 0.01632389939213203 0.22712445042119817 chrY 59373566 722634 0.012170971842924172 0.5212222900616865