BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524680.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 = 1,882,917 number of mapped reads = 1,744,277 (92.64%) number of supplementary alignments = 7,160 (0.38%) number of secondary alignments = 0 number of mapped bases = 103,400,376 bp number of sequenced bases = 103,369,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,128 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.014 >>>>>>> ACTG content number of A's = 27,011,143 bp (26.13%) number of C's = 19,434,031 bp (18.8%) number of T's = 31,267,577 bp (30.25%) number of G's = 25,642,028 bp (24.81%) number of N's = 14,285 bp (0.01%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 512,628 number of insertions = 6,884 mapped reads with insertion percentage = 0.39% number of deletions = 19,439 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3189X There is a 2.94% of reference with a coverageData >= 1X There is a 0.29% 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 8326329 0.03340544936897068 0.5799181266498972 chr2 243199373 8671366 0.035655379752973296 0.42921941192653046 chr3 198022430 6724579 0.03395867326746773 0.20360893306539363 chr4 191154276 6616773 0.034614831216226626 0.24631572114346728 chr5 180915260 6353102 0.03511645175757976 0.20933589879525039 chr6 171115067 5974372 0.034914353859908785 0.23032041864146283 chr7 159138663 5711752 0.035891667633276524 0.3793323012995081 chr8 146364022 5102733 0.03486330131048189 0.3584225294605422 chr9 141213431 4421245 0.03130895530751604 0.26515702825171855 chr10 135534747 4996917 0.03686816193341181 0.32960705803563417 chr11 135006516 4664949 0.03455350999502869 0.27002347138603777 chr12 133851895 4726256 0.03530959348763796 0.2111228738679925 chr13 115169878 3203407 0.027814625279016097 0.18608433531931776 chr14 107349540 3134024 0.029194573167244126 0.19465153908379232 chr15 102531392 3010580 0.029362519529628546 0.19192900777897703 chr16 90354753 3063121 0.03390105000895747 0.221046705423359 chr17 81195210 2774946 0.03417622788339361 0.21813529441412569 chr18 78077248 2811987 0.036015447163301656 0.4825523998583449 chr19 59128983 2126133 0.035957543866431796 0.41906293733011485 chr20 63025520 2190871 0.03476164893205165 0.21295773207835386 chr21 48129895 1361396 0.028285870974786045 0.22026386799658493 chr22 51304566 1239629 0.02416215741889328 0.17356074088605694 chrMT 16571 14571 0.8793072234626758 1.1873585258432247 chrX 155270560 5818249 0.03747168168904653 0.24040929495979577 chrY 59373566 361089 0.006081645828717783 0.21050701312457923