BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,364,962 number of mapped reads = 1,303,492 (95.5%) number of supplementary alignments = 36,308 (2.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 654,012 number of mapped paired reads (second in pair) = 649,480 number of mapped paired reads (both in pair) = 1,296,282 number of mapped paired reads (singletons) = 7,210 number of mapped bases = 160,870,005 bp number of sequenced bases = 160,729,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,276 duplication rate = 17.02% >>>>>>> Insert size mean insert size = 74,855.618 std insert size = 2,535,826.4328 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.2918 >>>>>>> ACTG content number of A's = 47,828,572 bp (29.76%) number of C's = 32,227,761 bp (20.05%) number of T's = 47,803,213 bp (29.74%) number of G's = 32,864,110 bp (20.45%) number of N's = 5,457 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,233,154 number of insertions = 26,483 mapped reads with insertion percentage = 1.92% number of deletions = 69,254 mapped reads with deletion percentage = 5.1% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.6833X There is a 3.13% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 12894126 0.05173157020940782 1.5061909790471277 chr2 243199373 14073066 0.057866374515694166 0.8125409589285839 chr3 198022430 10576785 0.05341205539190687 0.3422361530783744 chr4 191154276 10686085 0.05590293465368256 0.43728081074082337 chr5 180915260 9584292 0.052976691960645 0.34234896480817373 chr6 171115067 9102998 0.053198109082936575 0.4019852991520449 chr7 159138663 8572663 0.05386914052432375 0.9774515473249492 chr8 146364022 8007245 0.054707740950163286 0.4977717366043826 chr9 141213431 6871158 0.04865796370318345 0.9022986569930821 chr10 135534747 9457793 0.06978131593074062 0.741177073249201 chr11 135006516 7326260 0.054265973354945325 0.45580576160584524 chr12 133851895 7027889 0.052504964535616025 0.34440295509172275 chr13 115169878 5201570 0.04516432673480821 0.3148998118886154 chr14 107349540 4803313 0.044744607196267445 0.3232665874533593 chr15 102531392 4357870 0.04250278782911676 0.3034011773146511 chr16 90354753 4376983 0.0484421998253927 0.47313708469681964 chr17 81195210 4017703 0.049482019936890366 0.4384915460546666 chr18 78077248 4258668 0.054544289265933146 0.6953523250348848 chr19 59128983 2970030 0.050229681778900206 0.7525392076346022 chr20 63025520 3207872 0.05089798545097288 0.34545567535544475 chr21 48129895 2192441 0.045552582236051006 0.3496547238384699 chr22 51304566 1645486 0.03207289581204137 0.2673060803978289 chrMT 16571 195834 11.817874600205178 7.196215295089589 chrX 155270560 9048157 0.05827348725991585 0.3745060443644574 chrY 59373566 413718 0.006968050394682374 0.3624138928194715