BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251069.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 = 4,138,868 number of mapped reads = 3,920,198 (94.72%) number of supplementary alignments = 28,109 (0.68%) number of secondary alignments = 0 number of mapped bases = 304,477,199 bp number of sequenced bases = 304,287,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 819,589 duplication rate = 18.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1731 >>>>>>> ACTG content number of A's = 87,956,778 bp (28.91%) number of C's = 60,956,673 bp (20.03%) number of T's = 89,550,557 bp (29.43%) number of G's = 65,821,035 bp (21.63%) number of N's = 2,763 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,731,889 number of insertions = 36,099 mapped reads with insertion percentage = 0.9% number of deletions = 105,545 mapped reads with deletion percentage = 2.65% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0984X std coverageData = 1.0041X There is a 6.48% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.1% 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 0.01% 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 25526553 0.10241319719720979 2.108995454016434 chr2 243199373 26703617 0.10980133982500029 1.2414166227824353 chr3 198022430 20403523 0.10303642370210284 0.4531171994108513 chr4 191154276 18419021 0.09635683483219595 0.5047398876667932 chr5 180915260 18334117 0.1013409095506924 0.46915535645994794 chr6 171115067 17193955 0.10048182957494912 0.580885463424592 chr7 159138663 16505154 0.10371555025569117 1.529410147803797 chr8 146364022 14723500 0.10059507656874857 0.6295026414904613 chr9 141213431 12953934 0.09173301652871815 1.0442674936264762 chr10 135534747 18282228 0.13488960140974035 1.0235131928258039 chr11 135006516 14088038 0.10435080037173909 0.6366495634457471 chr12 133851895 13615322 0.10171930699972533 0.46804154548334015 chr13 115169878 8941860 0.07764061363336688 0.3876143332739954 chr14 107349540 9212451 0.08581733093593136 0.6394282167398959 chr15 102531392 8938963 0.0871826942523125 0.4130944735211589 chr16 90354753 8808183 0.09748444556093247 0.7948728664300523 chr17 81195210 8895313 0.10955465230030195 0.5674853057559416 chr18 78077248 7487066 0.0958930570913565 1.1780640727744076 chr19 59128983 6598158 0.11158923535011586 2.0469663128150453 chr20 63025520 6658372 0.10564564957179251 0.4951299158887259 chr21 48129895 3576106 0.07430113861665395 0.4226738720128254 chr22 51304566 3862518 0.0752860476395025 0.4141923837574429 chrMT 16571 208463 12.579989137650111 8.328807119901196 chrX 155270560 13766870 0.08866374926450964 0.49482022324096164 chrY 59373566 773914 0.013034655860151637 0.8873942605066162