BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013174.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 = 2,636,298 number of mapped reads = 2,384,344 (90.44%) number of supplementary alignments = 14,955 (0.57%) number of secondary alignments = 0 number of mapped bases = 155,558,430 bp number of sequenced bases = 155,490,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,182 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1196 >>>>>>> ACTG content number of A's = 42,462,337 bp (27.31%) number of C's = 29,958,207 bp (19.27%) number of T's = 47,139,212 bp (30.32%) number of G's = 35,893,966 bp (23.08%) number of N's = 36,907 bp (0.02%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,246,900 number of insertions = 10,867 mapped reads with insertion percentage = 0.45% number of deletions = 39,198 mapped reads with deletion percentage = 1.63% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.4048X There is a 4.37% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12146586 0.048732420209296086 0.6154142569373209 chr2 243199373 15367115 0.0631873133982134 0.5198054902436914 chr3 198022430 9668469 0.04882512046741372 0.24499643144202013 chr4 191154276 9371782 0.04902732073856407 0.2545215379071611 chr5 180915260 8649053 0.047807205428663124 0.24523269022221214 chr6 171115067 8158799 0.04768019054686751 0.3063584314508264 chr7 159138663 9542816 0.059965415192661256 0.7509452493247453 chr8 146364022 8253197 0.05638815391394478 0.38058564390519173 chr9 141213431 5530784 0.039166132858849664 0.3435667420174945 chr10 135534747 7292145 0.05380277132918542 0.4089995518253545 chr11 135006516 6543068 0.04846483113452094 0.3149297810358696 chr12 133851895 7836484 0.05854593242777773 0.27234667452279915 chr13 115169878 3901078 0.03387238110992876 0.20944491985082483 chr14 107349540 5068660 0.04721641098788127 0.2634987768807117 chr15 102531392 4421168 0.04312014022008011 0.23747718732976172 chr16 90354753 5226389 0.057842989178444215 0.30748401642622836 chr17 81195210 4228889 0.05208298617615497 0.28144468910252063 chr18 78077248 3683145 0.04717308939987229 0.6184150860846516 chr19 59128983 3378720 0.05714152059743696 0.5289369084166782 chr20 63025520 3555673 0.05641640084841823 0.26875741556838983 chr21 48129895 2574617 0.05349309405308281 0.2746642820654269 chr22 51304566 1633877 0.031846619655646245 0.1972152742396046 chrMT 16571 437418 26.39659646370165 19.256776171283498 chrX 155270560 8730919 0.05623035686868135 0.29720761652957267 chrY 59373566 357579 0.00602252861146996 0.11806643537995261