BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234085.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 = 727,688 number of mapped reads = 468,135 (64.33%) number of supplementary alignments = 2,174 (0.3%) number of secondary alignments = 0 number of mapped bases = 28,739,820 bp number of sequenced bases = 28,718,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,089 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3458 >>>>>>> ACTG content number of A's = 7,617,727 bp (26.53%) number of C's = 4,961,110 bp (17.28%) number of T's = 9,158,106 bp (31.89%) number of G's = 6,976,314 bp (24.29%) number of N's = 5,076 bp (0.02%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 284,932 number of insertions = 2,466 mapped reads with insertion percentage = 0.52% number of deletions = 11,911 mapped reads with deletion percentage = 2.51% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1218X There is a 0.84% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 2496430 0.010015742347939827 0.15372256635277615 chr2 243199373 2053253 0.008442673904426554 0.12751666630904573 chr3 198022430 2381652 0.012027182981241065 0.11883404940928381 chr4 191154276 1426149 0.007460722458544428 0.09632697548489011 chr5 180915260 1715107 0.009480167676292204 0.10642004059545114 chr6 171115067 1840442 0.010755581213663669 0.12065603162483449 chr7 159138663 1768806 0.011114872820063846 0.16583109407428676 chr8 146364022 1438491 0.009828173483781417 0.1539655652868267 chr9 141213431 1157028 0.008193469925675838 0.1108619657315399 chr10 135534747 1420887 0.010483562565693947 0.12029344677531059 chr11 135006516 1344048 0.009955430595661027 0.131932650864874 chr12 133851895 1128719 0.008432596340903504 0.09918190710946416 chr13 115169878 1069421 0.00928559636053448 0.10677807112651537 chr14 107349540 1167824 0.01087870520916997 0.11592607495007258 chr15 102531392 689299 0.006722809342137869 0.0897861954496052 chr16 90354753 788002 0.008721201418147865 0.10372810690532436 chr17 81195210 762074 0.009385701447166649 0.1106361218899948 chr18 78077248 658233 0.008430535359033146 0.14927516759451817 chr19 59128983 734387 0.012420085087544969 0.1366200564952387 chr20 63025520 668437 0.010605814914339462 0.11463090920386039 chr21 48129895 422156 0.008771180572905882 0.10268129408560955 chr22 51304566 285053 0.0055560941690842875 0.07972127504734391 chrMT 16571 21311 1.2860418803934583 1.6050509764868572 chrX 155270560 1191158 0.007671499349264922 0.09843249780478641 chrY 59373566 111453 0.0018771484939947855 0.04988066171974437