BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716420.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 = 662,014 number of mapped reads = 575,702 (86.96%) number of supplementary alignments = 2,399 (0.36%) number of secondary alignments = 0 number of mapped bases = 32,701,960 bp number of sequenced bases = 32,693,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,178 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.245 >>>>>>> ACTG content number of A's = 7,921,887 bp (24.23%) number of C's = 6,173,922 bp (18.88%) number of T's = 10,464,267 bp (32.01%) number of G's = 8,133,035 bp (24.88%) number of N's = 485 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 162,640 number of insertions = 1,832 mapped reads with insertion percentage = 0.32% number of deletions = 5,340 mapped reads with deletion percentage = 0.92% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.1303X There is a 0.99% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 3969969 0.0159276192936747 0.18944200417254056 chr2 243199373 2813561 0.011568948411721439 0.1763910899140359 chr3 198022430 2261289 0.011419357897991657 0.11461600712662535 chr4 191154276 1533174 0.0080206105355446 0.09793826178433862 chr5 180915260 1468613 0.008117684489412335 0.09529721816420282 chr6 171115067 2448046 0.014306431589685788 0.13613054565113072 chr7 159138663 1888443 0.011866651160692484 0.16032218562952222 chr8 146364022 2346334 0.016030811178446572 0.13854749301962604 chr9 141213431 1382576 0.009790683437186651 0.12002336728666005 chr10 135534747 1671493 0.012332579187239711 0.15319773383332314 chr11 135006516 1101960 0.008162272700970967 0.10791295927265425 chr12 133851895 1467743 0.010965425629573642 0.11202684005117466 chr13 115169878 792555 0.006881617083939257 0.08753680254435593 chr14 107349540 722170 0.006727276148551731 0.09101246621410444 chr15 102531392 991264 0.009667907366360539 0.10364675518829183 chr16 90354753 748694 0.008286160662737909 0.10304176378517235 chr17 81195210 828292 0.010201242166871667 0.10719726777230339 chr18 78077248 637099 0.008159854712092312 0.14822212125430617 chr19 59128983 774187 0.013093189849045771 0.1453285324531546 chr20 63025520 592421 0.009399700311873666 0.10298383175182856 chr21 48129895 297196 0.006174873225881752 0.0851478449826719 chr22 51304566 431539 0.008411317620345917 0.09661057140171966 chrMT 16571 59466 3.5885583247842616 2.659224910227486 chrX 155270560 1387627 0.008936832584361131 0.10520895959184481 chrY 59373566 86249 0.001452649820628931 0.04877518427093078