BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238492.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 = 2,298,820 number of mapped reads = 1,929,097 (83.92%) number of supplementary alignments = 19,053 (0.83%) number of secondary alignments = 0 number of mapped bases = 116,473,459 bp number of sequenced bases = 116,420,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 827,813 duplication rate = 23.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.156 >>>>>>> ACTG content number of A's = 29,524,793 bp (25.36%) number of C's = 18,992,898 bp (16.31%) number of T's = 41,169,125 bp (35.36%) number of G's = 26,731,043 bp (22.96%) number of N's = 2,500 bp (0%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 699,177 number of insertions = 7,437 mapped reads with insertion percentage = 0.38% number of deletions = 32,859 mapped reads with deletion percentage = 1.69% homopolymer indels = 41.47% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.8913X There is a 1.07% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 4049951 0.01624850916620184 0.5208426921067094 chr2 243199373 8578451 0.03527332695878291 1.711072227118714 chr3 198022430 13730796 0.06933959955950444 0.7559833762201502 chr4 191154276 3608844 0.018879221932759694 0.37975737407705 chr5 180915260 16168448 0.08937028308170356 0.8580712633244197 chr6 171115067 8770445 0.0512546624547095 0.9279254281301097 chr7 159138663 3710783 0.02331792243346923 0.5451398786541645 chr8 146364022 9626734 0.06577254347383266 0.8817838761273932 chr9 141213431 4327020 0.030641702912805793 0.48905467307351114 chr10 135534747 5199660 0.03836403664072948 0.5777668426851036 chr11 135006516 14736603 0.10915475368611097 1.0272772108981418 chr12 133851895 2644900 0.01975989955166492 0.3893306355582877 chr13 115169878 6415203 0.05570209078453656 0.8365688515317743 chr14 107349540 776673 0.007234991412166275 0.25176097495975713 chr15 102531392 877651 0.008559827218575166 0.47408483227811093 chr16 90354753 803822 0.008896289052995363 0.3662823910211858 chr17 81195210 771845 0.009506041058333367 0.27924937894730895 chr18 78077248 2747148 0.035185000372963966 2.8699079935427823 chr19 59128983 683959 0.01156723767767154 0.44653110461243767 chr20 63025520 674199 0.010697238198114033 0.30957507956185404 chr21 48129895 596122 0.012385690847653003 0.29507047025546446 chr22 51304566 304770 0.0059404069415576 0.1757041538411947 chrMT 16571 18912 1.1412708949369381 2.845822274607539 chrX 155270560 6371518 0.041034939269878334 0.5769256672667727 chrY 59373566 279002 0.00469909454318442 0.3108487891193004