BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525097.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 = 2,894,250 number of mapped reads = 2,671,781 (92.31%) number of supplementary alignments = 10,253 (0.35%) number of secondary alignments = 0 number of mapped bases = 155,387,946 bp number of sequenced bases = 155,339,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,195 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4977 >>>>>>> ACTG content number of A's = 36,719,949 bp (23.64%) number of C's = 31,595,594 bp (20.34%) number of T's = 50,092,181 bp (32.25%) number of G's = 36,928,813 bp (23.77%) number of N's = 3,038 bp (0%) GC percentage = 44.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 777,828 number of insertions = 9,806 mapped reads with insertion percentage = 0.37% number of deletions = 29,971 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.4368X There is a 4.3% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 13063831 0.052412431100823616 0.7275320005337177 chr2 243199373 12129817 0.049876020856353113 0.6714490354291179 chr3 198022430 8903251 0.044960820852466055 0.24731387063362303 chr4 191154276 9501479 0.049705814585073685 0.31589275065644784 chr5 180915260 8864654 0.048998929111894705 0.2517279312155989 chr6 171115067 8248047 0.048201757709623545 0.31695591270391454 chr7 159138663 8795782 0.05527118196286467 0.5664773169683456 chr8 146364022 8155705 0.055722061259016235 0.5637804533887045 chr9 141213431 5122659 0.03627600408632519 0.2855271685576738 chr10 135534747 6780536 0.05002802713019415 0.45420343621251785 chr11 135006516 5564243 0.04121462552222294 0.3167032957160653 chr12 133851895 7704256 0.05755806445624098 0.27451625989135336 chr13 115169878 4680241 0.0406377177893685 0.23133938762173017 chr14 107349540 5203293 0.048470566338709976 0.2600601302521085 chr15 102531392 5718667 0.05577479139266928 0.2738006047755844 chr16 90354753 5338933 0.05908856836784225 0.3019653534859136 chr17 81195210 6823501 0.08403822097387272 0.3556526011720017 chr18 78077248 2893925 0.03706489501269307 0.5312141538653815 chr19 59128983 3999523 0.06764065263899431 0.5497200714693251 chr20 63025520 5130006 0.08139569495023603 0.3457930726740724 chr21 48129895 2004518 0.041648085872616175 0.2949213248324483 chr22 51304566 1434887 0.02796801750549844 0.19253034398680588 chrMT 16571 428858 25.8800313801219 14.65637567646996 chrX 155270560 8348831 0.053769568423015925 0.2936331570087708 chrY 59373566 548503 0.009238168379510841 0.34396884318108384