BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068129.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 = 3,357,347 number of mapped reads = 3,086,609 (91.94%) number of supplementary alignments = 20,485 (0.61%) number of secondary alignments = 0 number of mapped bases = 188,992,895 bp number of sequenced bases = 188,902,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,151,029 duplication rate = 23.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4452 >>>>>>> ACTG content number of A's = 47,891,066 bp (25.35%) number of C's = 32,985,265 bp (17.46%) number of T's = 62,612,564 bp (33.15%) number of G's = 45,394,850 bp (24.03%) number of N's = 19,230 bp (0.01%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,199,057 number of insertions = 12,308 mapped reads with insertion percentage = 0.4% number of deletions = 50,638 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.6858X There is a 1.91% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 15386599 0.06173143697002063 0.7678735168782496 chr2 243199373 18603732 0.07649580576838083 0.9769909544979357 chr3 198022430 14068590 0.07104543662048789 0.6397590803245424 chr4 191154276 10893266 0.05698677648204951 0.5964010783025877 chr5 180915260 13119970 0.07251997426861614 0.643613965119519 chr6 171115067 11366518 0.06642616690206479 0.6697131164295657 chr7 159138663 10324508 0.06487743333623458 0.7202551752311886 chr8 146364022 9532756 0.06513045945129876 0.8276034331506462 chr9 141213431 7762542 0.05497028112007278 0.6024001223855111 chr10 135534747 6970961 0.05143301739442506 0.6081198494394489 chr11 135006516 9227817 0.06835090092984845 0.729020614776478 chr12 133851895 7987632 0.059675150658121054 0.5840704234904203 chr13 115169878 5870022 0.050968379075646844 0.5477536440427563 chr14 107349540 6206052 0.05781163105123692 0.5836933545941322 chr15 102531392 5664621 0.05524767478042237 0.5767848148165217 chr16 90354753 5229513 0.05787756400595772 0.5791592811120593 chr17 81195210 5082617 0.06259749805438031 0.6253647195013919 chr18 78077248 5239508 0.06710671974504019 0.9947098771556694 chr19 59128983 3417583 0.057798778646336604 0.6732577388457981 chr20 63025520 3407520 0.054065718140841997 0.5607049437650764 chr21 48129895 2672511 0.05552704820984962 0.5705485885547863 chr22 51304566 2193659 0.042757578341077865 0.4791480806544259 chrMT 16571 239351 14.443968378492547 12.917222639495124 chrX 155270560 7028455 0.0452658572236746 0.5117837775653956 chrY 59373566 1496592 0.025206368773605412 0.38185041785807095