BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525003.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,539,448 number of mapped reads = 1,418,966 (92.17%) number of supplementary alignments = 4,170 (0.27%) number of secondary alignments = 0 number of mapped bases = 82,196,746 bp number of sequenced bases = 82,170,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,193 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2822 >>>>>>> ACTG content number of A's = 19,925,572 bp (24.25%) number of C's = 15,296,939 bp (18.62%) number of T's = 26,470,239 bp (32.21%) number of G's = 20,476,802 bp (24.92%) number of N's = 699 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 405,352 number of insertions = 4,535 mapped reads with insertion percentage = 0.32% number of deletions = 15,842 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0266X std coverageData = 0.257X There is a 2.42% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 8567203 0.03437184214678446 0.48804221915930757 chr2 243199373 7631585 0.031379953434337186 0.2940303631248068 chr3 198022430 4401764 0.02222861319296001 0.16296245076268068 chr4 191154276 5128960 0.026831521153102535 0.1903029213811952 chr5 180915260 3489847 0.019289953760672263 0.15249569575172614 chr6 171115067 6562312 0.03835028741215407 0.308144651615581 chr7 159138663 5105952 0.03208492457926456 0.32865927582688415 chr8 146364022 5822566 0.039781402016951954 0.25826528115121783 chr9 141213431 2272212 0.016090622428117336 0.18967681758861551 chr10 135534747 4195232 0.0309531842782722 0.2508236778236604 chr11 135006516 3372800 0.024982497881805944 0.232291077726765 chr12 133851895 3397949 0.025385886393315536 0.17385246477385546 chr13 115169878 1575976 0.01368392523607605 0.12672585161666447 chr14 107349540 1862032 0.017345505160059373 0.14443951945672487 chr15 102531392 2274924 0.02218758524218612 0.1701798543366056 chr16 90354753 2734849 0.030267904113467057 0.19532525295132316 chr17 81195210 2123072 0.026147749356150444 0.22128785211447266 chr18 78077248 1594698 0.020424618449666667 0.31026188655747544 chr19 59128983 2065675 0.03493506729178819 0.3071230161988061 chr20 63025520 1928471 0.03059825607150881 0.18962438912388804 chr21 48129895 1092711 0.0227033738594277 0.1729585329836743 chr22 51304566 1108660 0.021609382681455683 0.15646796217105285 chrMT 16571 70214 4.237161305895842 3.1196524048166467 chrX 155270560 3578588 0.023047434104700854 0.18989921472412902 chrY 59373566 238494 0.00401683806561324 0.11171631841342801