BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,204,285 number of mapped reads = 1,040,648 (86.41%) number of supplementary alignments = 5,913 (0.49%) number of secondary alignments = 0 number of mapped bases = 67,672,494 bp number of sequenced bases = 67,637,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,788 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0876 >>>>>>> ACTG content number of A's = 18,276,892 bp (27.02%) number of C's = 12,106,670 bp (17.9%) number of T's = 21,678,103 bp (32.05%) number of G's = 15,538,160 bp (22.97%) number of N's = 37,726 bp (0.06%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 553,373 number of insertions = 4,751 mapped reads with insertion percentage = 0.45% number of deletions = 19,935 mapped reads with deletion percentage = 1.89% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.0219X std coverageData = 0.2274X There is a 1.96% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5528456 0.022180309833611207 0.3587261107943386 chr2 243199373 5632105 0.023158386185477543 0.22033412370104896 chr3 198022430 4919762 0.02484446837663794 0.17082705432803166 chr4 191154276 3641023 0.01904756239928423 0.1611391857233162 chr5 180915260 3456186 0.019103894276248447 0.1514353904387773 chr6 171115067 7896694 0.04614844349153661 0.29786337620291026 chr7 159138663 5193219 0.03263329540477539 0.41623460614412 chr8 146364022 3013355 0.020588085506423156 0.24699774960554918 chr9 141213431 2974003 0.021060340924653264 0.19571989113769342 chr10 135534747 1964436 0.014493965890532853 0.17844606232322055 chr11 135006516 4638460 0.034357304650391836 0.24693208934365826 chr12 133851895 2680152 0.020023265266434966 0.15618281398643527 chr13 115169878 3848593 0.033416662992384175 0.20085516327438657 chr14 107349540 1422660 0.013252595213728909 0.13373022233541118 chr15 102531392 1559763 0.01521254095526178 0.13930812601793224 chr16 90354753 1349257 0.014932883497562104 0.14062674196938252 chr17 81195210 1434380 0.017665820434481293 0.1695485890432595 chr18 78077248 1359064 0.017406658595343936 0.2737121520741492 chr19 59128983 1490376 0.025205507086093464 0.2691638223355575 chr20 63025520 671624 0.010656381732352229 0.1163037249499358 chr21 48129895 637464 0.013244658023874766 0.13738067944559246 chr22 51304566 535119 0.010430241238177514 0.10938706637858917 chrMT 16571 41840 2.524892885160823 2.3048781639707343 chrX 155270560 1648695 0.010618207340786303 0.12344523341698943 chrY 59373566 135808 0.002287347874641722 0.0793213328061969