BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524452.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 = 3,659,200 number of mapped reads = 3,365,712 (91.98%) number of supplementary alignments = 7,462 (0.2%) number of secondary alignments = 0 number of mapped bases = 196,021,035 bp number of sequenced bases = 195,958,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,656 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4569 >>>>>>> ACTG content number of A's = 48,867,903 bp (24.94%) number of C's = 33,007,822 bp (16.84%) number of T's = 62,882,620 bp (32.09%) number of G's = 51,196,970 bp (26.13%) number of N's = 3,595 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 914,575 number of insertions = 12,732 mapped reads with insertion percentage = 0.38% number of deletions = 36,537 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.5311X There is a 5.04% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 19193461 0.07700466672056958 1.063610293420497 chr2 243199373 15396550 0.06330834578261844 0.593354390575916 chr3 198022430 10870595 0.05489577620070615 0.2878417286639779 chr4 191154276 11188449 0.05853098991099733 0.3613330477029121 chr5 180915260 10740615 0.059368209182575314 0.3009687219370835 chr6 171115067 8397388 0.04907450961054178 0.39140195106221715 chr7 159138663 9611218 0.06039524160134486 0.7129039493260674 chr8 146364022 18696282 0.1277382361083245 0.5579068932562178 chr9 141213431 8216517 0.05818509572223339 0.4462271510022079 chr10 135534747 10242865 0.07557371985207602 0.5393643947876152 chr11 135006516 6623501 0.049060602378628894 0.4953660473659107 chr12 133851895 8938617 0.0667799062538487 0.3176506465570842 chr13 115169878 4380894 0.03803853990363695 0.24070957637332688 chr14 107349540 4733305 0.04409245721965832 0.2666122703631012 chr15 102531392 5180717 0.05052810557765567 0.2976893626277966 chr16 90354753 5989530 0.06628904181720247 0.35723078266545316 chr17 81195210 6704632 0.08257423067198176 0.37895208348165527 chr18 78077248 4712107 0.060351858200739864 0.8479932656194135 chr19 59128983 3925873 0.06639507058661909 0.7293157443188325 chr20 63025520 5538269 0.08787343603035723 0.36670001349832165 chr21 48129895 2705683 0.05621626641820016 0.320196847332623 chr22 51304566 1545341 0.030120925299319364 0.2111046273437838 chrMT 16571 38995 2.3532074105364793 2.4801837703416347 chrX 155270560 11847393 0.076301605404141 0.40733126625791405 chrY 59373566 602238 0.01014320076378771 0.25686183711136773