BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238495.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 = 3,781,269 number of mapped reads = 3,315,958 (87.69%) number of supplementary alignments = 28,773 (0.76%) number of secondary alignments = 0 number of mapped bases = 203,718,370 bp number of sequenced bases = 203,623,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,423,386 duplication rate = 22.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0252 >>>>>>> ACTG content number of A's = 50,520,279 bp (24.81%) number of C's = 34,235,993 bp (16.81%) number of T's = 70,914,250 bp (34.83%) number of G's = 47,948,240 bp (23.55%) number of N's = 4,562 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,178,606 number of insertions = 13,463 mapped reads with insertion percentage = 0.4% number of deletions = 56,760 mapped reads with deletion percentage = 1.7% homopolymer indels = 41.63% >>>>>>> Coverage mean coverageData = 0.0658X std coverageData = 1.2545X There is a 1.75% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 12578799 0.05046647005144272 0.6483982467579043 chr2 243199373 22046590 0.0906523307525139 2.8884411554840943 chr3 198022430 21062936 0.10636641515812123 0.9663273823784851 chr4 191154276 31579728 0.16520544902694198 1.1994791430612153 chr5 180915260 7201491 0.039805879282930584 0.5810120177777912 chr6 171115067 17529460 0.10244252775239249 1.5130147151248468 chr7 159138663 16796527 0.10554648809635908 1.3697789328866945 chr8 146364022 3314746 0.02264727324861297 1.6683516531041966 chr9 141213431 2120319 0.015014995280441845 0.4529798082699539 chr10 135534747 19584187 0.14449569157346787 1.3546674271257895 chr11 135006516 2245214 0.016630412120256476 0.34464415166718454 chr12 133851895 2597477 0.01940560497854737 0.427574115455495 chr13 115169878 1876492 0.016293253345288774 0.651044573696929 chr14 107349540 1702721 0.0158614652657105 0.43442555354166057 chr15 102531392 1637308 0.015968845912089052 0.6036044774189379 chr16 90354753 3948334 0.043698132847532656 0.6484573618918643 chr17 81195210 2737499 0.03371503072656626 0.5279049189950918 chr18 78077248 2440985 0.0312637171842942 2.09968262457538 chr19 59128983 966037 0.01633779156999876 0.5209014568297482 chr20 63025520 5832053 0.0925347859089461 0.9089371130375279 chr21 48129895 5285826 0.10982417476705486 1.0032626345039368 chr22 51304566 696953 0.013584619349474665 0.3028208626401291 chrMT 16571 87311 5.268903506125159 6.918608178048552 chrX 155270560 17246137 0.1110715192886533 0.9817869680163246 chrY 59373566 603240 0.0101600769608482 0.4309985678398648