BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068175.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 = 3,463,765 number of mapped reads = 2,988,394 (86.28%) number of supplementary alignments = 20,551 (0.59%) number of secondary alignments = 0 number of mapped bases = 186,490,624 bp number of sequenced bases = 186,398,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,090,717 duplication rate = 19.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3904 >>>>>>> ACTG content number of A's = 46,618,354 bp (25.01%) number of C's = 33,031,925 bp (17.72%) number of T's = 61,375,127 bp (32.93%) number of G's = 45,353,871 bp (24.33%) number of N's = 19,542 bp (0.01%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,212,990 number of insertions = 12,115 mapped reads with insertion percentage = 0.4% number of deletions = 51,454 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.8025X There is a 1.91% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 16126373 0.06469942957534297 0.9698200419419819 chr2 243199373 17698203 0.07277240389924854 1.382421403090293 chr3 198022430 13431694 0.06782915450537598 0.7146862692866117 chr4 191154276 10297880 0.0538720881137914 0.6298784253690867 chr5 180915260 12290008 0.0679324010589267 0.7173031422251296 chr6 171115067 11014307 0.06436783851418532 0.7686597775963178 chr7 159138663 11105750 0.06978662375716956 0.8386239357154832 chr8 146364022 8975108 0.061320452098535524 0.7782027221838398 chr9 141213431 7614367 0.053920982912737246 0.6772163799725883 chr10 135534747 7565906 0.05582262974969806 0.6714087276654205 chr11 135006516 9088576 0.06731953589558595 0.7635295266906093 chr12 133851895 7675373 0.05734228118324362 0.6376160691331452 chr13 115169878 5538177 0.04808702671370373 0.6072055304779492 chr14 107349540 5859683 0.054585077868056074 0.6473008131762796 chr15 102531392 5251743 0.051220830006872435 0.6295239871556216 chr16 90354753 5026156 0.05562691317411935 0.6479267818465115 chr17 81195210 5357812 0.06598679897496416 0.6986658352135972 chr18 78077248 5215078 0.06679382449545353 1.068918496813502 chr19 59128983 3717070 0.06286375667919064 0.8174572946890564 chr20 63025520 3419412 0.05425440361301263 0.6429624558229557 chr21 48129895 2668670 0.05544724334013195 0.6318878981651004 chr22 51304566 2307257 0.04497176723023054 0.5923084962031196 chrMT 16571 201308 12.148210729587834 11.9330222961651 chrX 155270560 7666583 0.049375638240758586 0.574280237221478 chrY 59373566 1378130 0.02321117111274738 0.4119471242902184