BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081740.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,072,534 number of mapped reads = 3,663,447 (89.95%) number of supplementary alignments = 22,346 (0.55%) number of secondary alignments = 0 number of mapped bases = 244,468,753 bp number of sequenced bases = 244,376,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 180,873 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1936 >>>>>>> ACTG content number of A's = 67,077,593 bp (27.45%) number of C's = 46,347,306 bp (18.97%) number of T's = 75,890,175 bp (31.05%) number of G's = 55,058,720 bp (22.53%) number of N's = 2,755 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 2,007,774 number of insertions = 18,143 mapped reads with insertion percentage = 0.49% number of deletions = 52,237 mapped reads with deletion percentage = 1.41% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.079X std coverageData = 0.6001X There is a 6.37% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 19068543 0.07650349244265273 0.9651460600624292 chr2 243199373 20318458 0.08354650651175816 0.7915741238561189 chr3 198022430 16046824 0.08103538573887817 0.3419058593067746 chr4 191154276 16206711 0.08478340814097196 0.4081672652652268 chr5 180915260 15155570 0.08377165088229704 0.34755435473601776 chr6 171115067 14182221 0.08288119362393728 0.4468180803674752 chr7 159138663 13533264 0.08504070440757693 0.8452344001786158 chr8 146364022 12649997 0.08642832321183412 0.7711127048619936 chr9 141213431 10383652 0.07353161754139378 0.5864724598844279 chr10 135534747 11667489 0.08608485468305777 0.7047258914704001 chr11 135006516 11119386 0.08236184689041232 0.5208418593951355 chr12 133851895 11072198 0.08271977023560256 0.34985563234991934 chr13 115169878 7749330 0.06728608325867984 0.3085550561343351 chr14 107349540 7371877 0.06867171484852194 0.3526191933758033 chr15 102531392 6935839 0.0676460044549088 0.318566104778511 chr16 90354753 6916811 0.07655171167365152 0.4062929899249855 chr17 81195210 6582549 0.08107065675425927 0.39237363801560254 chr18 78077248 6681700 0.08557806750565798 1.1278442156829764 chr19 59128983 4895108 0.08278694730805704 0.7643390691359079 chr20 63025520 4947464 0.07849937612573446 0.3566615587026337 chr21 48129895 3242879 0.06737764543222045 0.3668080778023772 chr22 51304566 2721851 0.053052802356811674 0.27256480026298363 chrMT 16571 42553 2.5679198599963793 2.320725322452245 chrX 155270560 14325142 0.09225922802107496 0.43973937735638535 chrY 59373566 651337 0.010970151262263748 0.28096566244916515