BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083630.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 = 2,361,308 number of mapped reads = 1,944,482 (82.35%) number of supplementary alignments = 13,263 (0.56%) number of secondary alignments = 0 number of mapped bases = 115,674,461 bp number of sequenced bases = 115,639,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,850 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5398 >>>>>>> ACTG content number of A's = 34,579,263 bp (29.9%) number of C's = 22,733,028 bp (19.66%) number of T's = 33,760,281 bp (29.19%) number of G's = 24,551,512 bp (21.23%) number of N's = 15,700 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 953,526 number of insertions = 8,077 mapped reads with insertion percentage = 0.41% number of deletions = 22,375 mapped reads with deletion percentage = 1.14% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.2728X There is a 3.3% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9128128 0.03662228789391863 0.4660224410508315 chr2 243199373 10440344 0.042929156729363774 0.26883324964106614 chr3 198022430 8379304 0.04231492361749121 0.22635125787954744 chr4 191154276 7810325 0.04085875117959695 0.22871193555855124 chr5 180915260 7437606 0.04111099306935192 0.2238329254500065 chr6 171115067 6654474 0.03888888405133839 0.22569400824605856 chr7 159138663 6287447 0.03950923604278365 0.29690945586883366 chr8 146364022 5791634 0.03957006592781387 0.3486159877654432 chr9 141213431 4906230 0.03474336658529315 0.24846439260900516 chr10 135534747 5286416 0.039004138178676796 0.2686040432776885 chr11 135006516 5047477 0.0373869139768039 0.22512205060208815 chr12 133851895 5184522 0.03873327307020943 0.21919155417064937 chr13 115169878 4171690 0.036222057993323564 0.20888048360243125 chr14 107349540 3623355 0.033752869364880374 0.21097370856469763 chr15 102531392 2882927 0.028117505709861036 0.18533564333338196 chr16 90354753 3128758 0.03462748661379219 0.21713981671598848 chr17 81195210 2760384 0.033996882328403366 0.2110301580347061 chr18 78077248 3210473 0.04111918750005123 0.4060446386503148 chr19 59128983 1916005 0.03240382132058656 0.3524512562923365 chr20 63025520 2138848 0.033936221390954015 0.20714754849849643 chr21 48129895 1442891 0.029979101346470836 0.19902768760990164 chr22 51304566 998070 0.019453824051449922 0.15277967143457583 chrMT 16571 41372 2.4966507754510894 1.9492774088172582 chrX 155270560 6710053 0.04321523024068439 0.2408860051509757 chrY 59373566 295728 0.0049808023995055305 0.10408151266644591