BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708650.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,654,662 number of mapped reads = 4,423,168 (95.03%) number of supplementary alignments = 116 (0%) number of secondary alignments = 0 number of mapped bases = 220,621,525 bp number of sequenced bases = 220,599,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,644 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5171 >>>>>>> ACTG content number of A's = 68,052,256 bp (30.85%) number of C's = 42,034,518 bp (19.05%) number of T's = 68,050,389 bp (30.85%) number of G's = 42,455,237 bp (19.25%) number of N's = 7,241 bp (0%) GC percentage = 38.3% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 358,722 number of insertions = 14,634 mapped reads with insertion percentage = 0.33% number of deletions = 12,617 mapped reads with deletion percentage = 0.28% homopolymer indels = 49.11% >>>>>>> Coverage mean coverageData = 0.0713X std coverageData = 0.2787X There is a 6.6% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 16883421 0.06773672591973201 0.2724286066912405 chr2 243199373 21751448 0.08943875032112028 0.31231823379727364 chr3 198022430 18003242 0.09091516551938081 0.31331548334748577 chr4 191154276 15751496 0.08240200705737809 0.29756253346211414 chr5 180915260 14138752 0.0781512405310641 0.2897864392004527 chr6 171115067 15426285 0.09015152943837494 0.31232384042706046 chr7 159138663 12949991 0.08137551714884018 0.2970641509224711 chr8 146364022 12635712 0.0863307240901046 0.3058867006918562 chr9 141213431 9971935 0.0706160520949314 0.277867717360521 chr10 135534747 8740758 0.06449090136273321 0.26359900478217096 chr11 135006516 9346592 0.06923067328098445 0.2751249551809059 chr12 133851895 9850529 0.07359274965812027 0.2828977414442243 chr13 115169878 8156245 0.07081925536119783 0.2774084088412071 chr14 107349540 7376291 0.06871283286355954 0.27496263461072423 chr15 102531392 6688835 0.06523694713907717 0.26736975327871043 chr16 90354753 4678609 0.05178044147826955 0.23651379596625716 chr17 81195210 4323200 0.05324452021246081 0.24140933380556595 chr18 78077248 8095263 0.10368273994493249 0.3363005738527661 chr19 59128983 1508178 0.02550657771333561 0.16370940613293544 chr20 63025520 3565852 0.056577906854239364 0.24660796931755977 chr21 48129895 2745288 0.057039143758780275 0.25049511077068404 chr22 51304566 1149057 0.022396778485564033 0.1542641939304675 chrMT 16571 340 0.02051777201134512 0.14176315827123626 chrX 155270560 5788527 0.03728026098443903 0.19953451443824433 chrY 59373566 1095679 0.018453986745549357 0.1410309429876443