BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173969.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 = 7,259,002 number of mapped reads = 7,109,943 (97.95%) number of supplementary alignments = 928,227 (12.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,553,282 number of mapped paired reads (second in pair) = 3,556,661 number of mapped paired reads (both in pair) = 7,014,212 number of mapped paired reads (singletons) = 95,731 number of mapped bases = 808,963,470 bp number of sequenced bases = 808,414,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,797,703 duplication rate = 65.7% >>>>>>> Insert size mean insert size = 940,335.6497 std insert size = 8,757,814.2012 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.5445 >>>>>>> ACTG content number of A's = 241,083,064 bp (29.82%) number of C's = 160,981,402 bp (19.91%) number of T's = 239,173,304 bp (29.59%) number of G's = 167,170,950 bp (20.68%) number of N's = 6,266 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 6,759,677 number of insertions = 89,827 mapped reads with insertion percentage = 1.22% number of deletions = 227,194 mapped reads with deletion percentage = 3.11% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.2613X std coverageData = 4.6234X There is a 5.33% of reference with a coverageData >= 1X There is a 4.04% of reference with a coverageData >= 2X There is a 3.06% of reference with a coverageData >= 3X There is a 2.48% of reference with a coverageData >= 4X There is a 1.89% of reference with a coverageData >= 5X There is a 1.57% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 1.04% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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% 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 64619499 0.2592551173623756 2.180684926414106 chr2 243199373 72531571 0.298239136496458 14.994187831727842 chr3 198022430 53606543 0.2707094494295419 1.6169935734378813 chr4 191154276 54919628 0.28730525494496395 2.272249904316599 chr5 180915260 51582407 0.2851191602079338 1.6728673928579714 chr6 171115067 45105567 0.2635978689123851 1.7926133971800906 chr7 159138663 44937862 0.2823817993242786 2.179628344716431 chr8 146364022 41403975 0.28288355590556263 2.9255922672043133 chr9 141213431 34978931 0.24770257865910786 2.128161438161837 chr10 135534747 38851607 0.2866542186410692 2.744751129747374 chr11 135006516 37714505 0.2793532202549394 1.7045156164110022 chr12 133851895 38038111 0.28418059378240407 1.7348531211077043 chr13 115169878 27307332 0.23710480964475797 1.5225648329862893 chr14 107349540 25096725 0.23378511915374767 1.5342999596290825 chr15 102531392 24509182 0.23904076129191731 1.5765316193597996 chr16 90354753 25564893 0.2829391055941462 2.1488632329041333 chr17 81195210 22351415 0.2752799703332253 1.8460229749711305 chr18 78077248 22022400 0.28205912175593073 2.7303104919078396 chr19 59128983 15634344 0.2644108389281784 1.9911435384481946 chr20 63025520 17178404 0.2725626698518315 1.731031628934184 chr21 48129895 11466279 0.23823611084129728 2.0871113751331563 chr22 51304566 10489767 0.20446069069174078 1.8395420060881946 chrMT 16571 536997 32.405829461106755 31.471246581675494 chrX 155270560 22456472 0.14462800932771802 1.1899969168550588 chrY 59373566 6059054 0.10204968992430066 1.6871838930572571