BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238083.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 = 2,274,380 number of mapped reads = 1,810,688 (79.61%) number of supplementary alignments = 7,339 (0.32%) number of secondary alignments = 0 number of mapped bases = 112,773,214 bp number of sequenced bases = 112,713,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,025 duplication rate = 8.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5525 >>>>>>> ACTG content number of A's = 28,891,733 bp (25.63%) number of C's = 19,239,225 bp (17.07%) number of T's = 36,940,046 bp (32.77%) number of G's = 27,637,647 bp (24.52%) number of N's = 5,117 bp (0%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 878,260 number of insertions = 9,717 mapped reads with insertion percentage = 0.53% number of deletions = 36,859 mapped reads with deletion percentage = 2.01% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.3701X There is a 2.56% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 10080773 0.0404443245098274 0.5556366532269705 chr2 243199373 8305904 0.03415265383928436 0.48079994932943015 chr3 198022430 9018008 0.04554033601143062 0.3190197740122895 chr4 191154276 6758353 0.03535548951047268 0.2768350822878787 chr5 180915260 5951162 0.03289474862430068 0.2521287747823769 chr6 171115067 7794650 0.045552096239427006 0.3413798185484964 chr7 159138663 7663416 0.04815558868934321 0.5098121076055115 chr8 146364022 5406708 0.03694014366454073 0.35693467737489865 chr9 141213431 4064878 0.028785349744812873 0.33182669550218036 chr10 135534747 5407522 0.03989768026054603 0.4464364705933325 chr11 135006516 4377529 0.03242457571455292 0.28826532277124917 chr12 133851895 5492958 0.041037581126513005 0.30962550011901596 chr13 115169878 3894345 0.033813919643120575 0.2722607261348122 chr14 107349540 3587032 0.033414507411955376 0.26451668927468347 chr15 102531392 3302806 0.03221263201030178 0.2613788548443071 chr16 90354753 3097815 0.03428502538211797 0.27356756848140845 chr17 81195210 3001187 0.0369626114643955 0.2887159763120401 chr18 78077248 2842090 0.03640100122381363 0.6093437261547061 chr19 59128983 2191583 0.03706444604332194 0.3886297689989312 chr20 63025520 2430185 0.038558745727127676 0.28108292015643455 chr21 48129895 1459668 0.03032767887816917 0.25059491977182685 chr22 51304566 1202972 0.023447659609867864 0.2169957568306926 chrMT 16571 54851 3.310059742924386 3.076249787547904 chrX 155270560 5028661 0.03238644209179126 0.27235369099793266 chrY 59373566 358158 0.006032280425939045 0.13632723077747347