BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524945.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 = 3,178,886 number of mapped reads = 2,905,820 (91.41%) number of supplementary alignments = 10,347 (0.33%) number of secondary alignments = 0 number of mapped bases = 167,612,017 bp number of sequenced bases = 167,558,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,521 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0415 >>>>>>> ACTG content number of A's = 41,956,724 bp (25.04%) number of C's = 32,485,472 bp (19.39%) number of T's = 52,908,778 bp (31.58%) number of G's = 40,204,028 bp (23.99%) number of N's = 3,230 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 857,728 number of insertions = 11,508 mapped reads with insertion percentage = 0.39% number of deletions = 33,130 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.461X There is a 4.62% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14196354 0.05695614294979028 0.7485481580579991 chr2 243199373 13249034 0.05447807630655364 0.7414754831697832 chr3 198022430 9720873 0.04908975715528791 0.25838440477421015 chr4 191154276 10479802 0.05482379060147208 0.3407152162117626 chr5 180915260 9549795 0.0527860115282702 0.2657865420267559 chr6 171115067 9010866 0.052659687764374366 0.34731824927089905 chr7 159138663 9614077 0.060413207065840434 0.6439583389553339 chr8 146364022 8918250 0.060931982314615545 0.5886063485160894 chr9 141213431 5594744 0.039619064280082536 0.3087928488059093 chr10 135534747 7448343 0.05495522856585256 0.47283377155039186 chr11 135006516 6055870 0.04485613124036176 0.35045677697787586 chr12 133851895 8347387 0.062362860085021586 0.2919626604021167 chr13 115169878 5063395 0.0439645772655937 0.24239622501153588 chr14 107349540 5561064 0.051803333297934955 0.27128456527981887 chr15 102531392 6157101 0.06005088665918044 0.28771356120828573 chr16 90354753 5817667 0.0643869504020447 0.3166441090353185 chr17 81195210 7400225 0.09114115229211181 0.3753577433810254 chr18 78077248 3119709 0.03995669775656027 0.5591993638123127 chr19 59128983 4202856 0.07107945692216625 0.5896348881503457 chr20 63025520 4741922 0.07523812576238958 0.33363850879709656 chr21 48129895 2140195 0.04446706148018815 0.3017325853698801 chr22 51304566 1562121 0.030447991705065784 0.20000055952706533 chrMT 16571 37838 2.2833866393096374 2.2172446499034937 chrX 155270560 9025802 0.05812951276790655 0.31272762744676014 chrY 59373566 596727 0.010050381679955016 0.4007737770456266