BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234100.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 = 5,526,190 number of mapped reads = 5,246,438 (94.94%) number of supplementary alignments = 36,975 (0.67%) number of secondary alignments = 0 number of mapped bases = 341,780,319 bp number of sequenced bases = 341,643,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 655,449 duplication rate = 10.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1376 >>>>>>> ACTG content number of A's = 88,777,310 bp (25.99%) number of C's = 62,988,685 bp (18.44%) number of T's = 109,220,866 bp (31.97%) number of G's = 80,622,338 bp (23.6%) number of N's = 34,113 bp (0.01%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,808,777 number of insertions = 22,410 mapped reads with insertion percentage = 0.42% number of deletions = 78,943 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.1104X std coverageData = 1.0559X There is a 7.99% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 29130558 0.11687255936666252 2.170953887135851 chr2 243199373 20035363 0.08238246156991531 1.8067622873651195 chr3 198022430 40211098 0.2030633499447512 0.5982701237724106 chr4 191154276 11829063 0.06188228297859264 0.41673089286095943 chr5 180915260 22069880 0.1219901516323167 0.4687143556211838 chr6 171115067 24997642 0.14608673822977844 0.7673400534915108 chr7 159138663 21216324 0.13331973261582575 1.1390350323317504 chr8 146364022 15777670 0.10779746131873856 1.2521036054253254 chr9 141213431 11096154 0.07857718576358363 0.6873686444617104 chr10 135534747 16547422 0.12208988739987098 0.7666161274113951 chr11 135006516 13256975 0.09819507526584866 0.9353143925571028 chr12 133851895 11792277 0.0880994400564893 0.4076102745671343 chr13 115169878 11928254 0.10357095281458925 0.4738931652276112 chr14 107349540 16861855 0.15707431070501093 0.5547738260566591 chr15 102531392 7769973 0.07578140556211312 0.3943274110496898 chr16 90354753 8489431 0.09395666213596976 0.5071604163591933 chr17 81195210 8613471 0.10608348694461163 0.5306113510847456 chr18 78077248 6811037 0.0872345936168242 1.661131716973257 chr19 59128983 9956225 0.1683814686953097 1.1768039575292364 chr20 63025520 10288210 0.16323879596709395 0.5647192900695635 chr21 48129895 5761911 0.11971584396766292 0.48236774626158824 chr22 51304566 4310326 0.08401447153845917 0.37214123789751885 chrMT 16571 335982 20.275300223281636 11.836442657165929 chrX 155270560 11987958 0.0772068961430937 0.5174618089985195 chrY 59373566 705260 0.011878350038803463 0.2554824426289352