BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173968.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 = 2,872,014 number of mapped reads = 2,811,643 (97.9%) number of supplementary alignments = 353,137 (12.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,406,181 number of mapped paired reads (second in pair) = 1,405,462 number of mapped paired reads (both in pair) = 2,774,740 number of mapped paired reads (singletons) = 36,903 number of mapped bases = 317,758,359 bp number of sequenced bases = 317,534,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,231,306 duplication rate = 65.24% >>>>>>> Insert size mean insert size = 1,075,426.793 std insert size = 9,580,399.3987 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 52.5944 >>>>>>> ACTG content number of A's = 95,317,810 bp (30.02%) number of C's = 62,722,048 bp (19.75%) number of T's = 94,554,994 bp (29.78%) number of G's = 64,937,431 bp (20.45%) number of N's = 2,420 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,695,645 number of insertions = 36,257 mapped reads with insertion percentage = 1.24% number of deletions = 95,279 mapped reads with deletion percentage = 3.31% homopolymer indels = 41.36% >>>>>>> Coverage mean coverageData = 0.1026X std coverageData = 1.9809X There is a 2.24% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 0.99% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 24890631 0.09986186152771913 1.1381281412441 chr2 243199373 30074944 0.12366373987321094 5.996154834078799 chr3 198022430 21600591 0.10908153687438338 0.9890414185286643 chr4 191154276 21494920 0.11244802078086917 1.252594479712213 chr5 180915260 19351855 0.10696640515565133 0.9804969202038605 chr6 171115067 18830293 0.11004462278006179 1.0714433888473764 chr7 159138663 18688635 0.11743616948698381 1.2047394464579677 chr8 146364022 16117348 0.11011823657045992 1.4635350596480252 chr9 141213431 14122848 0.10001065691832103 1.1762621522540095 chr10 135534747 15369102 0.1133960282524451 1.3886044839016802 chr11 135006516 14018579 0.1038363140931657 0.9746759618951667 chr12 133851895 13844361 0.10343044452228338 0.9762402856671396 chr13 115169878 10537419 0.09149457464911094 0.9221475923053322 chr14 107349540 10789062 0.10050403569498295 0.955871566667305 chr15 102531392 8880383 0.08661135703687706 0.8885903182461539 chr16 90354753 9438725 0.10446296057054132 1.0883920612911822 chr17 81195210 8609038 0.10602889012787824 0.9854665537512584 chr18 78077248 8227307 0.10537393684777414 1.408594054673558 chr19 59128983 6469597 0.1094149885852087 1.0286969578154097 chr20 63025520 6453393 0.10239333209785496 0.9792095530206074 chr21 48129895 4603066 0.09563839688409875 1.0196040703391072 chr22 51304566 4031869 0.07858694292433932 0.8793477042774814 chrMT 16571 317111 19.136503530263713 18.812068808018815 chrX 155270560 8435941 0.05433058913421836 0.6946693468635287 chrY 59373566 2561341 0.04313941662186839 0.8352420073128732