BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716115.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 = 1,112,909 number of mapped reads = 906,988 (81.5%) number of supplementary alignments = 2,960 (0.27%) number of secondary alignments = 0 number of mapped bases = 50,888,062 bp number of sequenced bases = 50,874,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,928 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.7661 >>>>>>> ACTG content number of A's = 12,593,296 bp (24.75%) number of C's = 10,460,863 bp (20.56%) number of T's = 15,352,627 bp (30.18%) number of G's = 12,465,760 bp (24.5%) number of N's = 1,558 bp (0%) GC percentage = 45.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 265,385 number of insertions = 4,145 mapped reads with insertion percentage = 0.45% number of deletions = 8,570 mapped reads with deletion percentage = 0.94% homopolymer indels = 35.46% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.1582X There is a 1.52% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4790789 0.019220770567307834 0.19635382657306452 chr2 243199373 4273667 0.017572689219063076 0.18808558325114455 chr3 198022430 3308151 0.016705940837106182 0.139196061732866 chr4 191154276 3255312 0.017029762912549234 0.15727128497690088 chr5 180915260 4285224 0.02368636012241311 0.16306018325730684 chr6 171115067 2113958 0.012354014389627068 0.1211565446039067 chr7 159138663 2804484 0.01762289532368385 0.17435896428930983 chr8 146364022 3051674 0.02084989164891902 0.1614058864490457 chr9 141213431 2147153 0.015205019698161714 0.14540676674165587 chr10 135534747 2592315 0.019126571284336407 0.22459291479140997 chr11 135006516 2030731 0.015041725837884743 0.15577166884945612 chr12 133851895 2313847 0.017286621156913765 0.13960888909178767 chr13 115169878 849165 0.007373151858335736 0.09085466658394496 chr14 107349540 2231274 0.020785128655418553 0.15463203881197088 chr15 102531392 948733 0.00925309782198217 0.1027354661901059 chr16 90354753 1317965 0.014586559713134294 0.13893201100102978 chr17 81195210 1859180 0.022897656154839675 0.168223623649059 chr18 78077248 1321529 0.016925916753623284 0.18899640640151483 chr19 59128983 1246319 0.021077971187158758 0.1836290383938322 chr20 63025520 1207938 0.0191658553551006 0.1528666977642502 chr21 48129895 676384 0.014053303045851232 0.1409680100823343 chr22 51304566 523534 0.010204432876403243 0.10809268373647318 chrMT 16571 13832 0.8347112425321345 1.1930074004836773 chrX 155270560 1557557 0.010031244815501406 0.11176065593139498 chrY 59373566 167347 0.002818543861758278 0.09672412053541674