BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472432.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,751,470 number of mapped reads = 18,572,091 (99.04%) number of supplementary alignments = 66,463 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,309,457 number of mapped paired reads (second in pair) = 9,262,634 number of mapped paired reads (both in pair) = 18,476,090 number of mapped paired reads (singletons) = 96,001 number of mapped bases = 1,818,927,565 bp number of sequenced bases = 1,818,710,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,947,316 duplication rate = 48.32% >>>>>>> Insert size mean insert size = 19,194.115 std insert size = 1,387,539.6051 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.6085 >>>>>>> ACTG content number of A's = 492,766,660 bp (27.09%) number of C's = 418,452,150 bp (23.01%) number of T's = 492,662,447 bp (27.09%) number of G's = 414,593,029 bp (22.8%) number of N's = 236,159 bp (0.01%) GC percentage = 45.8% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,104,765 number of insertions = 107,539 mapped reads with insertion percentage = 0.57% number of deletions = 89,634 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.5876X std coverageData = 18.9596X There is a 4.85% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199603743 0.8008154290616591 24.273416462873033 chr2 243199373 151827441 0.6242920741411615 18.440453743369822 chr3 198022430 142305580 0.7186336416536248 17.30553900986279 chr4 191154276 47910676 0.25063878769837195 8.709450488998785 chr5 180915260 94627193 0.5230470497624137 26.0511972111208 chr6 171115067 130757760 0.7641510609933607 18.300357514598424 chr7 159138663 107876364 0.6778765258320664 21.965009138514183 chr8 146364022 135261002 0.9241410570146809 22.710129197773977 chr9 141213431 46600644 0.3300014996448886 9.45926497513085 chr10 135534747 50412576 0.37195314940160695 16.656570881446527 chr11 135006516 59663195 0.441928262188471 14.297465438054573 chr12 133851895 87025536 0.6501628983287835 17.562628263999 chr13 115169878 81617254 0.7086684072027931 27.301515313164064 chr14 107349540 32301871 0.3009036741098285 8.94921114989828 chr15 102531392 28328833 0.2762942397192852 8.569392006556164 chr16 90354753 83675029 0.9260722454744578 25.041657984082732 chr17 81195210 70596391 0.8694649721332084 20.800605557487877 chr18 78077248 3880539 0.04970127789340116 2.896955327450374 chr19 59128983 38638908 0.6534681646731519 12.45325541255562 chr20 63025520 85967815 1.3640159573455324 31.64100649841367 chr21 48129895 16198723 0.33656260833313684 16.461509558134313 chr22 51304566 19261484 0.37543410853529097 11.229639405449522 chrMT 16571 20594 1.2427735200048278 1.526172910985151 chrX 155270560 104155225 0.6707982826879738 21.46440715942827 chrY 59373566 413189 0.006959140705815109 0.6419016262651739