BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237837.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 = 1,412,271 number of mapped reads = 1,089,780 (77.17%) number of supplementary alignments = 7,466 (0.53%) number of secondary alignments = 0 number of mapped bases = 69,535,405 bp number of sequenced bases = 69,505,926 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,116 duplication rate = 5.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5619 >>>>>>> ACTG content number of A's = 18,744,453 bp (26.97%) number of C's = 12,432,403 bp (17.89%) number of T's = 22,496,354 bp (32.37%) number of G's = 15,778,139 bp (22.7%) number of N's = 54,577 bp (0.08%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 554,705 number of insertions = 5,736 mapped reads with insertion percentage = 0.52% number of deletions = 17,945 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.93% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2571X There is a 1.69% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 6676863 0.02678774870534826 0.482769039356918 chr2 243199373 4484905 0.018441268761001287 0.2444201667041698 chr3 198022430 5341511 0.026974272560941707 0.21088526077411932 chr4 191154276 4931170 0.025796807182069 0.21738632367252594 chr5 180915260 4231175 0.023387606993462023 0.19606738849591726 chr6 171115067 4937860 0.028856956237524076 0.2315255065889998 chr7 159138663 2888462 0.01815059863862247 0.2142109712177937 chr8 146364022 3200876 0.021869281509632195 0.28019490747206577 chr9 141213431 2596410 0.01838642388060099 0.2218882234892412 chr10 135534747 4003279 0.029536920152291278 0.27674016318848776 chr11 135006516 4850693 0.035929325070502525 0.27784903023278607 chr12 133851895 2522810 0.01884777200950349 0.1757645159113255 chr13 115169878 1761819 0.015297567650458048 0.15703740420318776 chr14 107349540 1900942 0.0177079659586804 0.1805270487421855 chr15 102531392 1638405 0.015979545074351474 0.16241123333148022 chr16 90354753 1792002 0.019832957763716092 0.19620751886345647 chr17 81195210 1814311 0.022345049664875553 0.2359124424111052 chr18 78077248 1841442 0.023584873278320467 0.3654709414538374 chr19 59128983 1060310 0.01793215350921899 0.3207089001821353 chr20 63025520 1705152 0.027054945361815342 0.21690067312474864 chr21 48129895 754468 0.015675662704022104 0.16804414183062716 chr22 51304566 649398 0.012657703799696893 0.14282805318235187 chrMT 16571 108074 6.52187556574739 4.567968129676881 chrX 155270560 3650141 0.023508261965436334 0.20879979480220173 chrY 59373566 192927 0.0032493753196498254 0.09017358538466688