BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085110.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 = 2,066,143 number of mapped reads = 1,744,408 (84.43%) number of supplementary alignments = 12,153 (0.59%) number of secondary alignments = 0 number of mapped bases = 107,212,993 bp number of sequenced bases = 107,175,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,085 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9642 >>>>>>> ACTG content number of A's = 31,794,071 bp (29.67%) number of C's = 20,566,194 bp (19.19%) number of T's = 31,762,465 bp (29.64%) number of G's = 23,050,538 bp (21.51%) number of N's = 2,352 bp (0%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 938,570 number of insertions = 8,250 mapped reads with insertion percentage = 0.47% number of deletions = 23,156 mapped reads with deletion percentage = 1.31% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3033X There is a 3.12% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% 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 9337882 0.037463826419112514 0.5167333962463859 chr2 243199373 9719685 0.03996591307001437 0.32176371242902774 chr3 198022430 6762374 0.034149535484439816 0.20398480135442235 chr4 191154276 5431450 0.028413960250619767 0.18766079270613878 chr5 180915260 5766600 0.03187459145237389 0.1937235746983774 chr6 171115067 8021669 0.04687879998317156 0.311151209890302 chr7 159138663 9289982 0.05837664980256872 0.32546980149724813 chr8 146364022 6983752 0.04771495005787693 0.5405354261139672 chr9 141213431 3682626 0.02607844008832276 0.2613228394034581 chr10 135534747 7269080 0.05363259356657817 0.38100989217795606 chr11 135006516 3475473 0.025743001915551986 0.22342871630873687 chr12 133851895 3797257 0.0283690940647497 0.18547574447069565 chr13 115169878 3486195 0.030270024250611777 0.18610081916884044 chr14 107349540 3725121 0.03470085665946962 0.20750983877578286 chr15 102531392 1894568 0.018477931129619308 0.1460751077538376 chr16 90354753 2933366 0.032464988311129574 0.2094538257203958 chr17 81195210 1817755 0.022387465960122525 0.1754992727719004 chr18 78077248 2505867 0.03209471471125622 0.46115813270722555 chr19 59128983 1479715 0.02502520633578291 0.3516571571649058 chr20 63025520 2691097 0.042698529103766224 0.2263706441176918 chr21 48129895 1313828 0.02729754552757699 0.1849095847048458 chr22 51304566 790025 0.015398726889142771 0.13193263473643754 chrMT 16571 14154 0.8541427795546437 0.9586988263446016 chrX 155270560 4783971 0.030810547730361765 0.20753362312727272 chrY 59373566 239501 0.004033798475233911 0.08797255009243876