BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524550.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 = 1,884,115 number of mapped reads = 1,684,819 (89.42%) number of supplementary alignments = 6,910 (0.37%) number of secondary alignments = 0 number of mapped bases = 97,803,788 bp number of sequenced bases = 97,773,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,780 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8732 >>>>>>> ACTG content number of A's = 24,890,865 bp (25.46%) number of C's = 18,202,541 bp (18.62%) number of T's = 31,524,711 bp (32.24%) number of G's = 23,153,513 bp (23.68%) number of N's = 1,409 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 507,056 number of insertions = 5,761 mapped reads with insertion percentage = 0.34% number of deletions = 18,264 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.2991X There is a 2.81% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 9681001 0.03884042880679523 0.5727272468430004 chr2 243199373 7761980 0.031916118467953454 0.34984738742223104 chr3 198022430 5278119 0.02665414720948531 0.18223775483886379 chr4 191154276 5545766 0.02901199029416428 0.2102871683082748 chr5 180915260 5337680 0.029503757726131008 0.189511090741317 chr6 171115067 4194586 0.02451324756808236 0.22418536597275948 chr7 159138663 4896241 0.03076713670768995 0.3817019125860585 chr8 146364022 8998862 0.06148274608086405 0.33320239520554806 chr9 141213431 4193949 0.02969936337004658 0.24785406750982372 chr10 135534747 5106878 0.03767947417941467 0.300114455282546 chr11 135006516 3391985 0.02512460213401848 0.267724921201083 chr12 133851895 4627065 0.034568543090107165 0.20539221444389408 chr13 115169878 2189670 0.01901252339609147 0.15082759912155802 chr14 107349540 2306024 0.021481452086334046 0.16386352476094188 chr15 102531392 2557217 0.024940820075865157 0.18217095941619715 chr16 90354753 3053596 0.03379563220099777 0.21625677465195525 chr17 81195210 3395816 0.041822861225434355 0.23812122601850783 chr18 78077248 2309584 0.029580755715160452 0.4496999345941541 chr19 59128983 1993377 0.03371235050668807 0.3877145898848719 chr20 63025520 2770385 0.04395655918427964 0.23282285019818982 chr21 48129895 1335447 0.027746725813551018 0.20211988752490392 chr22 51304566 791841 0.015434123348787318 0.13548370304705518 chrMT 16571 4073 0.24579083941826083 0.5238494922699276 chrX 155270560 5765508 0.0371320100861361 0.23867061516788463 chrY 59373566 317138 0.005341400582205219 0.16901898000568535