BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231802.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 = 3,334,042 number of mapped reads = 2,043,590 (61.29%) number of supplementary alignments = 17,778 (0.53%) number of secondary alignments = 0 number of mapped bases = 125,383,363 bp number of sequenced bases = 125,339,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,049 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6126 >>>>>>> ACTG content number of A's = 37,475,926 bp (29.9%) number of C's = 25,024,558 bp (19.97%) number of T's = 35,165,595 bp (28.06%) number of G's = 27,663,061 bp (22.07%) number of N's = 10,159 bp (0.01%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 733,118 number of insertions = 8,892 mapped reads with insertion percentage = 0.43% number of deletions = 26,711 mapped reads with deletion percentage = 1.3% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 4.3084X There is a 3.44% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 11757714 0.047172255590889785 0.8798761216547883 chr2 243199373 9353832 0.038461579421917344 15.306755537664198 chr3 198022430 10665251 0.05385880276289913 0.2590774341686376 chr4 191154276 7346803 0.03843389305086746 0.22745314664862076 chr5 180915260 6295397 0.03479749027251764 0.2126112689491685 chr6 171115067 10805488 0.06314749594785829 0.3427195233542361 chr7 159138663 9243418 0.05808404963160964 0.6717103381821414 chr8 146364022 6238461 0.042622913163728175 0.5661564753603477 chr9 141213431 3706116 0.026244784038991307 0.25281436883135 chr10 135534747 5483207 0.040456097948078217 0.31545079767194223 chr11 135006516 2997497 0.02220260983551342 0.2479391413687764 chr12 133851895 5232102 0.03908874058152109 0.22557438216850592 chr13 115169878 4379520 0.038026609700845565 0.21908264500579902 chr14 107349540 5426168 0.05054672800647306 0.27420787549565534 chr15 102531392 3422087 0.033375992788628094 0.20491120529969972 chr16 90354753 2871319 0.03177828398247074 0.22456046758362436 chr17 81195210 3883594 0.04783033383373231 0.2759478176023328 chr18 78077248 1346337 0.01724365336237261 0.5037064925651897 chr19 59128983 3028717 0.05122220688287502 0.4851185529899598 chr20 63025520 2790987 0.04428344264355137 0.23824533155674216 chr21 48129895 2920687 0.06068342762850407 0.28433741996187467 chr22 51304566 1143139 0.022281428128638685 0.16422749126974273 chrMT 16571 169408 10.223160943817513 6.0532842485398195 chrX 155270560 4575483 0.029467807677128234 0.21846065105506887 chrY 59373566 300631 0.005063381236020083 0.13102183806324777