BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524296.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 = 2,107,316 number of mapped reads = 1,915,084 (90.88%) number of supplementary alignments = 7,950 (0.38%) number of secondary alignments = 0 number of mapped bases = 110,478,794 bp number of sequenced bases = 110,448,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,033 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5128 >>>>>>> ACTG content number of A's = 26,110,049 bp (23.64%) number of C's = 20,534,074 bp (18.59%) number of T's = 35,631,476 bp (32.26%) number of G's = 28,157,804 bp (25.49%) number of N's = 14,860 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 566,850 number of insertions = 6,947 mapped reads with insertion percentage = 0.36% number of deletions = 19,286 mapped reads with deletion percentage = 1% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3393X There is a 3.2% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9436307 0.037858710089231834 0.6781506988735764 chr2 243199373 7178841 0.029518336792751516 0.4369083529644194 chr3 198022430 7822747 0.03950434806804461 0.21883517853747228 chr4 191154276 5848936 0.030597986727746544 0.21092672148141375 chr5 180915260 6562673 0.03627484491910743 0.20848484184916882 chr6 171115067 7240335 0.04231266788447098 0.24595943749613888 chr7 159138663 5082589 0.03193811550371012 0.4226501271892406 chr8 146364022 11535424 0.07881324824484531 0.4045172436914537 chr9 141213431 4525658 0.03204835381416375 0.25964770828576494 chr10 135534747 5616762 0.041441491014846545 0.33305854914192723 chr11 135006516 5318428 0.03939386155257869 0.2811589304225822 chr12 133851895 4439087 0.03316416999550137 0.20229554256166343 chr13 115169878 2876301 0.02497442082902962 0.17514741418133883 chr14 107349540 2356008 0.021947071221730435 0.17311915675089062 chr15 102531392 3369354 0.032861682010520255 0.2088622577468715 chr16 90354753 3382601 0.03743689056401936 0.22671171238730634 chr17 81195210 3304020 0.040692301922736575 0.24921917453306897 chr18 78077248 2622910 0.03359378137917976 0.4660093466851621 chr19 59128983 1899231 0.032120136414319864 0.45512933437100156 chr20 63025520 2464315 0.039100272397593866 0.21730328950247416 chr21 48129895 1591703 0.03307098426040614 0.21244313206242835 chr22 51304566 771229 0.015032365735244696 0.1338161270725497 chrMT 16571 50081 3.0222074708828677 2.681920405108164 chrX 155270560 4884540 0.03145824939383229 0.22708913961893654 chrY 59373566 298714 0.005031094140446272 0.13463633308386794