BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524477.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 = 1,171,420 number of mapped reads = 1,052,038 (89.81%) number of supplementary alignments = 4,051 (0.35%) number of secondary alignments = 0 number of mapped bases = 60,607,812 bp number of sequenced bases = 60,591,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,616 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4265 >>>>>>> ACTG content number of A's = 14,746,915 bp (24.34%) number of C's = 10,732,086 bp (17.71%) number of T's = 19,935,169 bp (32.9%) number of G's = 15,175,303 bp (25.05%) number of N's = 1,814 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 290,259 number of insertions = 4,198 mapped reads with insertion percentage = 0.4% number of deletions = 9,909 mapped reads with deletion percentage = 0.94% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.1927X There is a 1.81% of reference with a coverageData >= 1X There is a 0.1% 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 4357151 0.01748100358795094 0.30194431265409216 chr2 243199373 5145256 0.021156534807349196 0.20593553324644417 chr3 198022430 3620376 0.01828265616172875 0.14164145016170762 chr4 191154276 3724310 0.019483268059355366 0.1627716222805987 chr5 180915260 3401241 0.01880018855236424 0.14589657997392178 chr6 171115067 3115192 0.01820524664844388 0.15102105692989398 chr7 159138663 3838859 0.024122729999308843 0.2500636937592432 chr8 146364022 2622813 0.017919793157911444 0.18592509686862346 chr9 141213431 2805135 0.019864505664478897 0.1929652827118246 chr10 135534747 2299459 0.016965826482857566 0.1901163095327301 chr11 135006516 2289767 0.016960418414174915 0.16413669247293014 chr12 133851895 4565260 0.03410680140165367 0.2088269649560865 chr13 115169878 2239994 0.019449477926858617 0.14653627289925425 chr14 107349540 2119120 0.019740373363500208 0.15502963886556811 chr15 102531392 1765735 0.01722140863941455 0.13813782544721742 chr16 90354753 1704372 0.018863113930486865 0.15170225251178127 chr17 81195210 1768395 0.02177954832557241 0.15821210768039376 chr18 78077248 1842182 0.02359435107139022 0.31553717034802653 chr19 59128983 998256 0.016882685095395603 0.2287591681258105 chr20 63025520 1729918 0.02744789729620636 0.17876767514526096 chr21 48129895 740496 0.01538536495872264 0.14060117198735997 chr22 51304566 602584 0.011745231408837958 0.11296603811151755 chrMT 16571 7476 0.451149598696518 0.7585573962972697 chrX 155270560 3127870 0.02014464300251123 0.1668967935068099 chrY 59373566 176595 0.002974303413071063 0.08370166214181925