BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,693,574 number of mapped reads = 10,416,792 (97.41%) number of supplementary alignments = 1,017,901 (9.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,220,849 number of mapped paired reads (second in pair) = 5,195,943 number of mapped paired reads (both in pair) = 10,226,600 number of mapped paired reads (singletons) = 190,192 number of mapped bases = 1,223,221,149 bp number of sequenced bases = 1,222,530,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,280,105 duplication rate = 65.83% >>>>>>> Insert size mean insert size = 952,929.2569 std insert size = 8,771,725.6388 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.7312 >>>>>>> ACTG content number of A's = 368,724,146 bp (30.16%) number of C's = 238,294,693 bp (19.49%) number of T's = 368,404,462 bp (30.13%) number of G's = 247,093,148 bp (20.21%) number of N's = 14,228 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 12,323,214 number of insertions = 126,188 mapped reads with insertion percentage = 1.17% number of deletions = 280,392 mapped reads with deletion percentage = 2.62% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.3951X std coverageData = 5.6306X There is a 7.47% of reference with a coverageData >= 1X There is a 6.01% of reference with a coverageData >= 2X There is a 4.76% of reference with a coverageData >= 3X There is a 3.99% of reference with a coverageData >= 4X There is a 3.15% of reference with a coverageData >= 5X There is a 2.6% of reference with a coverageData >= 6X There is a 2% of reference with a coverageData >= 7X There is a 1.65% of reference with a coverageData >= 8X There is a 1.26% of reference with a coverageData >= 9X There is a 1.06% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.69% of reference with a coverageData >= 12X There is a 0.53% of reference with a coverageData >= 13X There is a 0.47% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 112463177 0.4512052028147204 3.100955005031595 chr2 243199373 92469794 0.3802221726944995 16.99122890770767 chr3 198022430 76220385 0.38490783594565525 1.8734245611116949 chr4 191154276 78167043 0.4089212370012586 2.702313169564396 chr5 180915260 63224121 0.34946814878965987 1.7621407942530156 chr6 171115067 60532860 0.3537552891236632 1.9298464392941952 chr7 159138663 108474947 0.6816379184987874 6.282201246273665 chr8 146364022 111833133 0.7640752930388863 3.6472413374338783 chr9 141213431 44655395 0.31622625895974443 2.4799653903688013 chr10 135534747 56669524 0.4181180490933443 7.388915611352584 chr11 135006516 49200635 0.3644315582516032 1.9032805069206258 chr12 133851895 47224811 0.3528139142146624 1.7885661014643637 chr13 115169878 31064202 0.2697250577967965 1.5682533526208133 chr14 107349540 40298246 0.37539281491099075 1.8705213293434773 chr15 102531392 29379100 0.2865376098668396 1.5841000536021392 chr16 90354753 28740254 0.31808237027663616 2.875110754305146 chr17 81195210 29828071 0.3673624466270855 2.138686984832569 chr18 78077248 21330793 0.2732011379294516 3.31975846574684 chr19 59128983 15873294 0.2684520043241738 2.0580126182065306 chr20 63025520 46422136 0.7365609359510242 2.66867536736906 chr21 48129895 14915420 0.3098992840104887 1.9195961004938793 chr22 51304566 12575922 0.24512286099447755 1.412362131099227 chrMT 16571 1787468 107.86723794580894 83.0932012614939 chrX 155270560 47537822 0.30616120660606877 1.6912512575076717 chrY 59373566 2332596 0.03928677620609818 1.596174136259171