BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008727.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 = 2,294,175 number of mapped reads = 1,858,823 (81.02%) number of supplementary alignments = 14,009 (0.61%) number of secondary alignments = 0 number of mapped bases = 120,176,908 bp number of sequenced bases = 120,110,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,579 duplication rate = 12.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1409 >>>>>>> ACTG content number of A's = 32,034,907 bp (26.67%) number of C's = 22,911,369 bp (19.08%) number of T's = 37,292,506 bp (31.05%) number of G's = 27,795,121 bp (23.14%) number of N's = 76,629 bp (0.06%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,091,001 number of insertions = 8,884 mapped reads with insertion percentage = 0.47% number of deletions = 39,307 mapped reads with deletion percentage = 2.09% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.4124X There is a 1.83% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 10537457 0.04227655264297215 0.5165982579943748 chr2 243199373 15985468 0.06572988985460912 0.5774212940431236 chr3 198022430 7020267 0.03545187785040311 0.33332646356312245 chr4 191154276 7474853 0.039103770820172495 0.36405118008545656 chr5 180915260 4821857 0.02665257203842285 0.2866894878445472 chr6 171115067 4453001 0.026023430186892894 0.3074770020569703 chr7 159138663 6651752 0.041798466033361105 0.516047565282223 chr8 146364022 7155514 0.048888476158437354 0.43499071140811196 chr9 141213431 4200072 0.02974272326829875 0.35454387658500963 chr10 135534747 5771236 0.04258122826613606 0.41269342198602843 chr11 135006516 5232708 0.03875892923568222 0.41107071714176036 chr12 133851895 6962065 0.052013197123582 0.4143021252775915 chr13 115169878 2118527 0.01839480111283959 0.2366410033693094 chr14 107349540 4087377 0.03807540302454952 0.3725498863761088 chr15 102531392 3940017 0.03842742133063014 0.37601400186053086 chr16 90354753 4031039 0.04461346931024204 0.38465372916105706 chr17 81195210 2460279 0.030300789911128993 0.319227780685809 chr18 78077248 2354742 0.03015913163332806 0.4679462010853765 chr19 59128983 2185405 0.036959962595669874 0.41728099626360554 chr20 63025520 2683505 0.04257806996277064 0.3752513682150505 chr21 48129895 2391342 0.049685169685078266 0.4109448138437342 chr22 51304566 1016075 0.019804767474302383 0.24707305625479975 chrMT 16571 441668 26.653068613843462 19.223426721874045 chrX 155270560 5924477 0.038155829411576796 0.35473586025905524 chrY 59373566 276205 0.004651986037018561 0.12334232145351133