BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505955.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 = 3,611,175 number of mapped reads = 2,477,317 (68.6%) number of supplementary alignments = 164 (0%) number of secondary alignments = 0 number of mapped bases = 115,206,086 bp number of sequenced bases = 115,182,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,720 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6341 >>>>>>> ACTG content number of A's = 33,750,830 bp (29.3%) number of C's = 23,911,891 bp (20.76%) number of T's = 33,323,540 bp (28.93%) number of G's = 24,195,547 bp (21.01%) number of N's = 334 bp (0%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 604,777 number of insertions = 4,978 mapped reads with insertion percentage = 0.2% number of deletions = 17,306 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.0372X std coverageData = 0.3788X There is a 2.98% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12138112 0.04869842230001906 0.7922270774866457 chr2 243199373 7552563 0.03105502660979311 0.2979718645176407 chr3 198022430 7375866 0.03724762896809215 0.23433660094266098 chr4 191154276 5308598 0.02777127517670596 0.20736730805326548 chr5 180915260 6783713 0.03749663240126897 0.23680694089433635 chr6 171115067 8015379 0.0468420410927344 0.30996155755482796 chr7 159138663 7735861 0.04861082061497526 0.5286802821433093 chr8 146364022 7537151 0.051495927052346235 0.5653750748491259 chr9 141213431 3269713 0.02315440519252025 0.24143828004397078 chr10 135534747 3830135 0.028259432247289325 0.30041217054287284 chr11 135006516 6539298 0.04843690655642132 0.39315217120940077 chr12 133851895 3325604 0.02484540095603428 0.1959315134193297 chr13 115169878 3294407 0.028604762436233545 0.20212212343232017 chr14 107349540 4171023 0.038854595930266675 0.2438628042372361 chr15 102531392 2384851 0.02325971542452091 0.18110834386299193 chr16 90354753 3920378 0.04338873019773514 0.26712640586930114 chr17 81195210 1992024 0.024533762521212765 0.22070261107566755 chr18 78077248 2761647 0.035370701077988814 0.41651060878433416 chr19 59128983 3143572 0.053164655309562825 0.5661390867119713 chr20 63025520 3069721 0.048706000363027545 0.2706837188476012 chr21 48129895 1814923 0.03770885018552399 0.2523805466936131 chr22 51304566 960412 0.018719815308446425 0.16253322237682585 chrMT 16571 22842 1.37843220083278 1.5817086548622505 chrX 155270560 7903667 0.05090254714093902 0.3122145375398297 chrY 59373566 354626 0.00597279267342642 0.1197893210996795