BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716824.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 = 892,990 number of mapped reads = 771,845 (86.43%) number of supplementary alignments = 4,230 (0.47%) number of secondary alignments = 0 number of mapped bases = 44,908,078 bp number of sequenced bases = 44,894,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,240 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1166 >>>>>>> ACTG content number of A's = 11,550,305 bp (25.73%) number of C's = 8,727,916 bp (19.44%) number of T's = 14,048,403 bp (31.29%) number of G's = 10,567,825 bp (23.54%) number of N's = 314 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 226,847 number of insertions = 3,576 mapped reads with insertion percentage = 0.46% number of deletions = 8,319 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1601X There is a 1.3% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 3641503 0.014609805124617924 0.20592598926924918 chr2 243199373 3738394 0.015371725485492925 0.20092315895730695 chr3 198022430 2948210 0.014888262910418785 0.1334133491819649 chr4 191154276 2839213 0.014852992354719808 0.15497033453998996 chr5 180915260 2694615 0.014894348879138222 0.1339017583990846 chr6 171115067 2543975 0.014867042654987244 0.14146640476556144 chr7 159138663 2460598 0.01546197481877801 0.1931221113157353 chr8 146364022 2229571 0.015233053653035034 0.18042081096199808 chr9 141213431 1859663 0.013169165190809648 0.1379743634148956 chr10 135534747 2149660 0.01586058223135946 0.18268149296761638 chr11 135006516 2062005 0.015273373916263419 0.152733990947489 chr12 133851895 2001493 0.014953041942364732 0.13412553584666845 chr13 115169878 1373084 0.01192224932286548 0.11978449986403132 chr14 107349540 1359579 0.012664972760945227 0.12476605671927402 chr15 102531392 1312139 0.012797436710895333 0.12466091075706777 chr16 90354753 1384863 0.015326952418319377 0.13981480234376065 chr17 81195210 1278275 0.015743231651226715 0.14280622585810326 chr18 78077248 1179944 0.01511252035932414 0.21887687781951862 chr19 59128983 994737 0.016823171134196575 0.17965690233073273 chr20 63025520 998347 0.01584036117433065 0.1427498455382563 chr21 48129895 607803 0.012628388239783196 0.1339480956439368 chr22 51304566 560851 0.01093179503750212 0.11352741518540733 chrMT 16571 17086 1.031078389958361 1.3414005504587143 chrX 155270560 2513727 0.016189334282042906 0.1450409355938213 chrY 59373566 158743 0.0026736308881969463 0.09534964924379002