BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,666,100 number of mapped reads = 13,546,704 (99.13%) number of supplementary alignments = 66,506 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,795,162 number of mapped paired reads (second in pair) = 6,751,542 number of mapped paired reads (both in pair) = 13,475,638 number of mapped paired reads (singletons) = 71,066 number of mapped bases = 1,337,254,097 bp number of sequenced bases = 1,337,085,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,215,625 duplication rate = 46.31% >>>>>>> Insert size mean insert size = 29,375.3001 std insert size = 1,655,215.0806 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 55.1884 >>>>>>> ACTG content number of A's = 363,378,387 bp (27.18%) number of C's = 307,290,095 bp (22.98%) number of T's = 361,715,568 bp (27.05%) number of G's = 304,442,079 bp (22.77%) number of N's = 259,030 bp (0.02%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 7,891,581 number of insertions = 78,417 mapped reads with insertion percentage = 0.57% number of deletions = 70,376 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.432X std coverageData = 14.3764X There is a 3.92% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 130643753 0.5241461484663663 15.017076192923332 chr2 243199373 105390491 0.4333501756190794 20.819529794903374 chr3 198022430 138359740 0.6987074141045537 15.492998035537568 chr4 191154276 72051347 0.37692772826070603 15.847374163212692 chr5 180915260 74498672 0.41178766235639824 13.590392817074981 chr6 171115067 63070167 0.3685833638483746 11.366811392726207 chr7 159138663 45426582 0.2854528317860758 9.143823965072823 chr8 146364022 47702455 0.32591653569071777 9.983202527747284 chr9 141213431 76930884 0.5447844688371037 14.085954989168247 chr10 135534747 37216491 0.27459003557220646 9.201160437532813 chr11 135006516 72392766 0.5362168297121304 16.65672454956129 chr12 133851895 81088438 0.6058071721733936 17.198386414141726 chr13 115169878 35404858 0.30741421815172887 11.163351971014631 chr14 107349540 30437160 0.2835332130906197 10.230144841105787 chr15 102531392 27771306 0.27085661725922927 7.224277705773481 chr16 90354753 58867365 0.6515137615394732 19.202276199941632 chr17 81195210 41454561 0.5105542679180213 12.025908042876301 chr18 78077248 23479993 0.3007277228828557 11.089322012574957 chr19 59128983 29243875 0.49457767606116276 14.459460154706104 chr20 63025520 38898028 0.6171790093917512 21.20372006534451 chr21 48129895 8648895 0.17969902074376018 12.314526013009125 chr22 51304566 23105319 0.45035599755390193 13.773353752479911 chrMT 16571 2193 0.13233962947317604 0.41111666058351015 chrX 155270560 73210741 0.4715043276716462 15.875044920246685 chrY 59373566 1958017 0.032977924890009135 1.7220052384783329