BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068118.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 = 1,551,633 number of mapped reads = 1,060,596 (68.35%) number of supplementary alignments = 9,600 (0.62%) number of secondary alignments = 0 number of mapped bases = 69,671,971 bp number of sequenced bases = 69,645,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,289 duplication rate = 13.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7414 >>>>>>> ACTG content number of A's = 19,319,316 bp (27.74%) number of C's = 12,347,910 bp (17.73%) number of T's = 22,642,628 bp (32.51%) number of G's = 15,262,403 bp (21.91%) number of N's = 73,211 bp (0.11%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 618,486 number of insertions = 5,515 mapped reads with insertion percentage = 0.52% number of deletions = 16,267 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.4034X There is a 0.79% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 6958195 0.027916460035620132 0.5360918286231969 chr2 243199373 5297184 0.02178124036528663 0.40990353718826994 chr3 198022430 4718430 0.023827755269945936 0.3812176418276899 chr4 191154276 4917195 0.025723698694556013 0.39549973837797225 chr5 180915260 4413540 0.024395620358393207 0.37698788359077623 chr6 171115067 4386664 0.02563575538324746 0.3967796269755692 chr7 159138663 3475106 0.021836968681834407 0.3869954993082867 chr8 146364022 3276015 0.022382652206701454 0.4325689279148703 chr9 141213431 2737231 0.019383644888565876 0.3603653133639645 chr10 135534747 3646931 0.026907719833645316 0.596877893636282 chr11 135006516 3194003 0.023658139581944328 0.37783020629042763 chr12 133851895 2927640 0.021872234233217245 0.35214610170798877 chr13 115169878 2296072 0.019936393437874442 0.34684537637584767 chr14 107349540 2017369 0.018792525799365325 0.3372163059795946 chr15 102531392 1919224 0.018718403823094493 0.3532308142088971 chr16 90354753 1715708 0.01898857495631691 0.32656431100278854 chr17 81195210 1590566 0.01958940681353001 0.326379839894471 chr18 78077248 2180174 0.027923294632515736 0.5218101832092256 chr19 59128983 1168712 0.019765467638772006 0.4055119230633983 chr20 63025520 1276755 0.020257746385908437 0.32416678025707474 chr21 48129895 829586 0.017236397461494565 0.2952851187939328 chr22 51304566 711055 0.0138594876721109 0.2569315101034044 chrMT 16571 89748 5.415967654335888 4.8341996205865225 chrX 155270560 3730159 0.024023607566044717 0.37609611182676533 chrY 59373566 198709 0.0033467587242443884 0.13215158450727374