BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231852.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,453,371 number of mapped reads = 3,019,470 (87.44%) number of supplementary alignments = 28,561 (0.83%) number of secondary alignments = 0 number of mapped bases = 191,757,675 bp number of sequenced bases = 191,685,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 507,277 duplication rate = 13.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2305 >>>>>>> ACTG content number of A's = 48,865,326 bp (25.49%) number of C's = 34,526,861 bp (18.01%) number of T's = 62,702,594 bp (32.71%) number of G's = 45,517,960 bp (23.75%) number of N's = 73,019 bp (0.04%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,241,179 number of insertions = 12,151 mapped reads with insertion percentage = 0.4% number of deletions = 42,080 mapped reads with deletion percentage = 1.38% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.0619X std coverageData = 0.7169X There is a 3.97% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 13939123 0.05592412546085492 0.8107623049905107 chr2 243199373 16111395 0.06624768313033438 1.7569267716495882 chr3 198022430 14057926 0.07099158413519115 0.3930768118262206 chr4 191154276 5401693 0.028258290178138627 0.27746867812455944 chr5 180915260 13431849 0.0742438697542706 0.4026764486583885 chr6 171115067 12425997 0.0726177841487214 0.6199066948162033 chr7 159138663 13451498 0.08452690092036276 0.5558131189872164 chr8 146364022 13820031 0.09442232326739422 0.6936816934928034 chr9 141213431 4622989 0.03273760128383255 0.4073502511859533 chr10 135534747 12340458 0.09105014229303132 0.5554661701618401 chr11 135006516 5037195 0.03731075468979586 0.5630314819688437 chr12 133851895 9217815 0.06886577885206631 0.380652044342693 chr13 115169878 8865543 0.07697796640889035 0.46005240467360325 chr14 107349540 3062586 0.02852910222065227 0.27732872378607787 chr15 102531392 7811534 0.07618675458926764 0.42595099737609354 chr16 90354753 7127010 0.07887808624743847 0.4401126287217074 chr17 81195210 9489271 0.11686983751874033 0.5905121010081444 chr18 78077248 5499813 0.0704406615356115 1.143203213487994 chr19 59128983 1746576 0.029538407586005663 0.6555024021325212 chr20 63025520 2283163 0.03622600813130935 0.33981781303251346 chr21 48129895 2263930 0.04703791687058532 0.32449308941360244 chr22 51304566 1978917 0.03857194698811018 0.2787694388377601 chrMT 16571 516526 31.17047854685897 20.937432894155812 chrX 155270560 6849562 0.04411371994794119 0.3675144648153413 chrY 59373566 405275 0.006825849065558906 0.1947304575321791