BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231859.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 = 1,158,795 number of mapped reads = 965,866 (83.35%) number of supplementary alignments = 6,286 (0.54%) number of secondary alignments = 0 number of mapped bases = 64,236,123 bp number of sequenced bases = 64,196,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,028 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3111 >>>>>>> ACTG content number of A's = 18,094,605 bp (28.19%) number of C's = 11,383,230 bp (17.73%) number of T's = 20,953,965 bp (32.64%) number of G's = 13,761,901 bp (21.44%) number of N's = 3,009 bp (0%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 485,388 number of insertions = 4,713 mapped reads with insertion percentage = 0.48% number of deletions = 22,776 mapped reads with deletion percentage = 2.33% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.207X There is a 1.86% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5633858 0.022603185409917192 0.32393507389711906 chr2 243199373 5602592 0.023037033076561426 0.22692489963480225 chr3 198022430 6996152 0.035330098716594885 0.20458588440619416 chr4 191154276 3142201 0.01643803667776702 0.14188059438168982 chr5 180915260 3728896 0.02061128508451968 0.1558228406977083 chr6 171115067 6111541 0.03571597234041348 0.2402971647919946 chr7 159138663 4477911 0.02813842290480975 0.29259381176733185 chr8 146364022 1523544 0.010409279406109789 0.2842164206102569 chr9 141213431 2877714 0.020378472356499856 0.17633567240515702 chr10 135534747 2869845 0.021174238071953608 0.21374511956532857 chr11 135006516 3070555 0.0227437540866546 0.17827935583864823 chr12 133851895 2575879 0.019244247531945664 0.15209452677649477 chr13 115169878 2880212 0.025008379361138162 0.17321603147160192 chr14 107349540 2459809 0.022914015281295105 0.17002752824375622 chr15 102531392 873735 0.008521634037700376 0.10005790299337618 chr16 90354753 1571044 0.017387508103751885 0.14893862746597103 chr17 81195210 1229215 0.01513900881591414 0.1354418332158578 chr18 78077248 1276048 0.01634340390685901 0.2445415764733276 chr19 59128983 1232173 0.02083873148976704 0.22233908126004667 chr20 63025520 1423025 0.022578552307065455 0.16599522639678646 chr21 48129895 627377 0.013035079341020795 0.12570507886366086 chr22 51304566 496520 0.00967789104774807 0.105145634829432 chrMT 16571 42660 2.5743769235411262 2.5128930469221387 chrX 155270560 1410430 0.009083692362544452 0.10957363152919632 chrY 59373566 103187 0.0017379282895017625 0.051945560253044636