BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231834.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 = 5,152,676 number of mapped reads = 4,627,879 (89.82%) number of supplementary alignments = 24,314 (0.47%) number of secondary alignments = 0 number of mapped bases = 294,567,399 bp number of sequenced bases = 294,448,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 440,215 duplication rate = 7.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7414 >>>>>>> ACTG content number of A's = 74,684,724 bp (25.36%) number of C's = 52,965,309 bp (17.99%) number of T's = 96,013,327 bp (32.61%) number of G's = 70,673,768 bp (24%) number of N's = 111,263 bp (0.04%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,852,567 number of insertions = 19,409 mapped reads with insertion percentage = 0.42% number of deletions = 66,720 mapped reads with deletion percentage = 1.43% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.0952X std coverageData = 0.9625X There is a 7.42% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 21655170 0.08688110750985852 1.7142530689326694 chr2 243199373 27217133 0.1119128419792431 1.5217282996225447 chr3 198022430 26337720 0.13300372084111886 0.4550329768494519 chr4 191154276 9159613 0.04791738480388479 0.3462458914940257 chr5 180915260 14522892 0.08027455505964505 0.35895913165607013 chr6 171115067 26571864 0.15528652424277753 0.8123590864448971 chr7 159138663 22719628 0.14276623651161377 1.8596874168495843 chr8 146364022 10993138 0.07510819837951707 0.7507839232504402 chr9 141213431 15729376 0.11138725182592582 0.790842170732393 chr10 135534747 14354256 0.10590830999227084 0.8683193340284684 chr11 135006516 12805691 0.09485239216157537 0.6519682115251706 chr12 133851895 11211444 0.08376006929151059 0.3875647846376662 chr13 115169878 12269764 0.10653622468888957 0.4370323199378928 chr14 107349540 11216895 0.10448945566045276 0.47296553695859694 chr15 102531392 4735052 0.0461814855688295 0.3420879620346262 chr16 90354753 7246200 0.0801972199514507 0.4796446282358121 chr17 81195210 7428612 0.09149076651196542 0.440714781353461 chr18 78077248 7074735 0.09061199236940318 1.7529142081523144 chr19 59128983 4398627 0.07439037130065301 1.059121773988044 chr20 63025520 7573317 0.12016270551992272 0.4681623986821294 chr21 48129895 5461628 0.11347683181108124 0.4629922971933671 chr22 51304566 2605485 0.05078466115472061 0.2726814714977064 chrMT 16571 181162 10.932472391527368 6.460324991551774 chrX 155270560 10354260 0.06668527504505684 0.455238506127015 chrY 59373566 743737 0.012526399374428681 0.2756379795677668