BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819112.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 = 2,007,309 number of mapped reads = 1,840,106 (91.67%) number of supplementary alignments = 7,734 (0.39%) number of secondary alignments = 0 number of mapped bases = 107,613,457 bp number of sequenced bases = 107,579,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,538 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3496 >>>>>>> ACTG content number of A's = 27,413,933 bp (25.48%) number of C's = 20,262,654 bp (18.84%) number of T's = 34,492,577 bp (32.06%) number of G's = 25,408,365 bp (23.62%) number of N's = 1,655 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 553,675 number of insertions = 8,152 mapped reads with insertion percentage = 0.44% number of deletions = 20,497 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.3251X There is a 2.99% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 10622501 0.042617751391680586 0.6035298301116793 chr2 243199373 8702507 0.03578342695809499 0.4176940528135279 chr3 198022430 4686860 0.023668328885773193 0.17447022598000006 chr4 191154276 5887427 0.03079934764315709 0.24411040402998913 chr5 180915260 5851656 0.03234473421423931 0.20399864286245484 chr6 171115067 4569928 0.026706753999634642 0.2365718051276059 chr7 159138663 5338340 0.03354521082032717 0.3803500831348003 chr8 146364022 9881918 0.06751603204782115 0.38001449374512297 chr9 141213431 4625200 0.03275325843474478 0.29159683736025 chr10 135534747 5633634 0.041565975697730115 0.3329440139992626 chr11 135006516 3676889 0.027234900276961446 0.2787989889223829 chr12 133851895 4998886 0.03734639692624449 0.22045921295192292 chr13 115169878 3979042 0.03454932894866833 0.2111378895376801 chr14 107349540 2526869 0.023538703565939827 0.17622620852223533 chr15 102531392 2853751 0.027832948956744877 0.190918564026443 chr16 90354753 3365382 0.0372463195156983 0.230530070155034 chr17 81195210 2880613 0.03547762238683785 0.2297299008568562 chr18 78077248 2521652 0.03229688628369688 0.49211711581254663 chr19 59128983 2247935 0.03801748120714337 0.3852888737213052 chr20 63025520 4186929 0.0664322801303345 0.296612040821104 chr21 48129895 1506829 0.03130754804264584 0.23442489723804516 chr22 51304566 905724 0.017653867299062622 0.14920785196336286 chrMT 16571 18711 1.1291412708949369 1.3314782498676225 chrX 155270560 5772443 0.037176674058495056 0.24932281258249256 chrY 59373566 371831 0.0062625680930129745 0.222424291790621