BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525068.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 = 1,637,036 number of mapped reads = 1,469,068 (89.74%) number of supplementary alignments = 4,465 (0.27%) number of secondary alignments = 0 number of mapped bases = 85,401,235 bp number of sequenced bases = 85,373,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,586 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1902 >>>>>>> ACTG content number of A's = 21,411,436 bp (25.08%) number of C's = 15,532,363 bp (18.19%) number of T's = 27,952,346 bp (32.74%) number of G's = 20,468,109 bp (23.97%) number of N's = 8,901 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 419,452 number of insertions = 5,784 mapped reads with insertion percentage = 0.39% number of deletions = 17,512 mapped reads with deletion percentage = 1.18% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.2692X There is a 2.42% of reference with a coverageData >= 1X There is a 0.25% 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% 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 6913186 0.027735882752324217 0.50760345239884 chr2 243199373 7086206 0.029137435317318848 0.3219991516610034 chr3 198022430 5772525 0.029150864374303455 0.19043490386977632 chr4 191154276 5547616 0.029021668340811796 0.21272390473805083 chr5 180915260 5229061 0.028903371666934012 0.18941808944444552 chr6 171115067 5318265 0.03108005094606894 0.2184517840042204 chr7 159138663 4658939 0.02927597173541668 0.30742290706052094 chr8 146364022 4255503 0.02907478861164392 0.28330734864488877 chr9 141213431 3597751 0.02547739952582839 0.22075882448977568 chr10 135534747 4078178 0.030089538588949444 0.2939073924823104 chr11 135006516 3817801 0.02827864249159648 0.22144607983404407 chr12 133851895 3730723 0.02787202228253847 0.19049211566888644 chr13 115169878 2695957 0.023408525274290905 0.17124648305026424 chr14 107349540 2676027 0.024928164573411307 0.17951948000637863 chr15 102531392 2442455 0.02382153360406928 0.17211161311125267 chr16 90354753 2407549 0.026645515814757416 0.19735967982580432 chr17 81195210 2164117 0.026653259471833377 0.19100048681815446 chr18 78077248 2305708 0.029531112572000487 0.3491690466143826 chr19 59128983 1692185 0.02861853720704109 0.35495949858942044 chr20 63025520 1788892 0.028383613494977908 0.1925662491206352 chr21 48129895 1110763 0.02307844220312552 0.19247718369154065 chr22 51304566 994858 0.019391217538025758 0.1537169738185496 chrMT 16571 15640 0.9438175125218755 1.0865749238438656 chrX 155270560 4815929 0.031016369104355648 0.21633251744398044 chrY 59373566 285401 0.004806869777705452 0.16556810461868648