BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237284.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 = 3,051,564 number of mapped reads = 2,819,897 (92.41%) number of supplementary alignments = 31,812 (1.04%) number of secondary alignments = 0 number of mapped bases = 173,970,826 bp number of sequenced bases = 173,881,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,242,921 duplication rate = 22.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0864 >>>>>>> ACTG content number of A's = 44,284,834 bp (25.47%) number of C's = 29,784,842 bp (17.13%) number of T's = 58,331,959 bp (33.55%) number of G's = 41,462,169 bp (23.85%) number of N's = 17,913 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,068,518 number of insertions = 14,041 mapped reads with insertion percentage = 0.49% number of deletions = 51,145 mapped reads with deletion percentage = 1.79% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.8878X There is a 1.29% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% 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 0.03% 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 0.01% 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 10768409 0.04320313809769806 0.9658173694525942 chr2 243199373 12998061 0.053446112297337214 1.2866162386640283 chr3 198022430 13079185 0.06604900768059457 0.7471328114423913 chr4 191154276 9352414 0.04892599943722944 0.7572705919384468 chr5 180915260 11917257 0.06587203865500345 0.7461973455776751 chr6 171115067 6336497 0.037030619869377134 0.6354239669968013 chr7 159138663 8562041 0.05380239370240279 0.8776137409669023 chr8 146364022 7288626 0.0497979346317772 1.1450561282894087 chr9 141213431 7466646 0.05287489969704086 0.7927392689235065 chr10 135534747 9518347 0.07022809434985701 1.0534104271956994 chr11 135006516 11281679 0.08356395923882666 0.9751140709506384 chr12 133851895 9738002 0.07275206675258501 0.8020515916062475 chr13 115169878 5538141 0.04808671413197121 0.6467483761567193 chr14 107349540 5893178 0.054897095972651584 0.7084400687145641 chr15 102531392 5470409 0.05335350367622045 0.6719364985956531 chr16 90354753 4504891 0.04985781987583985 0.6896765486305082 chr17 81195210 3824550 0.04710314807979436 0.6528184957125458 chr18 78077248 4699971 0.06019642239439587 1.4340835868362487 chr19 59128983 4146127 0.07012004586650848 0.9197444971256212 chr20 63025520 3451974 0.054771051472482894 0.7191372531259682 chr21 48129895 2327007 0.04834847447724538 0.7110268526655837 chr22 51304566 2040956 0.039781176591572764 0.5725914007502958 chrMT 16571 111623 6.736044897712872 10.006644392277321 chrX 155270560 12874749 0.08291815911528883 0.8652074364044565 chrY 59373566 780086 0.013138607844440403 0.5382379265866195