BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716889.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 = 4,804,322 number of mapped reads = 4,153,477 (86.45%) number of supplementary alignments = 17,179 (0.36%) number of secondary alignments = 0 number of mapped bases = 234,589,990 bp number of sequenced bases = 234,519,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,167 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0693 >>>>>>> ACTG content number of A's = 56,001,926 bp (23.88%) number of C's = 45,170,976 bp (19.26%) number of T's = 73,877,572 bp (31.5%) number of G's = 59,466,024 bp (25.36%) number of N's = 3,443 bp (0%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,211,439 number of insertions = 13,255 mapped reads with insertion percentage = 0.32% number of deletions = 43,699 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.58% >>>>>>> Coverage mean coverageData = 0.0758X std coverageData = 0.546X There is a 6.21% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 20481180 0.08217102897408629 0.8388792854213518 chr2 243199373 22640667 0.09309508787261553 0.9259712367950198 chr3 198022430 14523096 0.07334066145941144 0.3312565719696384 chr4 191154276 13736995 0.07186339373334238 0.35455466582751377 chr5 180915260 12414280 0.06861930828831134 0.31324364550465894 chr6 171115067 13762587 0.08042884382589173 0.4230304928849457 chr7 159138663 11843686 0.07442368671904702 0.8282385320196151 chr8 146364022 17323099 0.11835626517560442 0.5771151920163722 chr9 141213431 10316115 0.07305335566841373 0.42655066640826395 chr10 135534747 11653481 0.08598150111277368 0.6463241012362301 chr11 135006516 6602296 0.048903535885630886 0.38807920525934425 chr12 133851895 11108015 0.08298735703368264 0.3560313402988928 chr13 115169878 6472273 0.056197619658848647 0.28093086694968195 chr14 107349540 6213232 0.057878515362059305 0.31510036783272777 chr15 102531392 5954306 0.05807300460721337 0.2993719666562967 chr16 90354753 7723542 0.0854801960445844 0.39222850363348816 chr17 81195210 10664569 0.1313448046996861 0.4807520825897022 chr18 78077248 4854414 0.06217450184719625 0.665601612908428 chr19 59128983 5247935 0.08875402101876165 0.710332629780184 chr20 63025520 5560768 0.08823041840828921 0.3604887725845098 chr21 48129895 2551900 0.05302110050312805 0.29539105013785094 chr22 51304566 3635964 0.07087018336730497 0.32535857160986137 chrMT 16571 11170 0.6740691569609559 0.9959195026023026 chrX 155270560 8760356 0.05641994206757546 0.35642934938349274 chrY 59373566 534064 0.008994979348217016 0.20249616529143907