BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238639.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 = 3,847,064 number of mapped reads = 3,513,652 (91.33%) number of supplementary alignments = 25,176 (0.65%) number of secondary alignments = 0 number of mapped bases = 218,590,075 bp number of sequenced bases = 218,505,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,276,761 duplication rate = 20.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.883 >>>>>>> ACTG content number of A's = 53,620,966 bp (24.54%) number of C's = 38,550,671 bp (17.64%) number of T's = 73,069,847 bp (33.44%) number of G's = 53,253,164 bp (24.37%) number of N's = 11,183 bp (0.01%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,127,175 number of insertions = 13,906 mapped reads with insertion percentage = 0.39% number of deletions = 48,701 mapped reads with deletion percentage = 1.37% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.0706X std coverageData = 0.923X There is a 2.35% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 22306587 0.08949460952396182 0.9965428051876701 chr2 243199373 22349569 0.0918981357735655 1.9397805744115557 chr3 198022430 12829858 0.06478992304053637 0.6297765635778154 chr4 191154276 11068031 0.05790103800764572 0.6062249785248128 chr5 180915260 3528994 0.019506336834162027 0.32194234532611143 chr6 171115067 15123368 0.08838127620871633 0.9378226134194544 chr7 159138663 18594445 0.11684429571963917 1.0632327552735938 chr8 146364022 9117156 0.062290963827162385 0.7299365064236882 chr9 141213431 8477558 0.060033652181427415 0.6641193332364956 chr10 135534747 9798632 0.07229608802826039 0.7377628044158252 chr11 135006516 8260798 0.06118814294859665 0.6439204641438203 chr12 133851895 9736268 0.07273911213584237 0.6814687883702478 chr13 115169878 7233672 0.06280871461893882 0.7208921126494201 chr14 107349540 8267310 0.07701299884470861 0.6986025172450434 chr15 102531392 6372049 0.062147298263540596 0.7106291888720726 chr16 90354753 6471638 0.07162476555051842 0.7105994869085555 chr17 81195210 4235203 0.05216074938410776 0.5890797226060488 chr18 78077248 5851716 0.07494777479861996 1.6191363227441056 chr19 59128983 3524716 0.0596106312195493 0.7066475028139169 chr20 63025520 3317290 0.05263407584737103 0.5781371007789664 chr21 48129895 3114526 0.06471084135961651 0.6469791371788648 chr22 51304566 1881798 0.03667895758050073 0.48236100415416067 chrMT 16571 7870 0.4749260756743709 1.103927074896781 chrX 155270560 16466539 0.10605061899693026 0.8405063932943262 chrY 59373566 654484 0.011023154647642353 0.3683395668768469