BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063560.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 = 2,542,475 number of mapped reads = 2,304,673 (90.65%) number of supplementary alignments = 21,974 (0.86%) number of secondary alignments = 0 number of mapped bases = 152,674,962 bp number of sequenced bases = 152,606,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,927 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8032 >>>>>>> ACTG content number of A's = 42,840,187 bp (28.07%) number of C's = 27,956,766 bp (18.32%) number of T's = 48,652,120 bp (31.88%) number of G's = 33,152,588 bp (21.72%) number of N's = 4,494 bp (0%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,229,728 number of insertions = 11,823 mapped reads with insertion percentage = 0.51% number of deletions = 41,759 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.4465X There is a 3.78% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 19580013 0.07855552343839496 0.7458297985458517 chr2 243199373 18446185 0.07584799571008763 0.6013304714329476 chr3 198022430 6574146 0.0331989966995153 0.2383764410173045 chr4 191154276 7160491 0.037459224820061046 0.2538985979752057 chr5 180915260 8309946 0.045932808542518744 0.2642566756165441 chr6 171115067 2600418 0.01519689671745855 0.18317771850660855 chr7 159138663 14864446 0.0934056232456848 0.8348288659289561 chr8 146364022 9170683 0.06265667528595245 0.6075446825309594 chr9 141213431 4826140 0.03417621090163867 0.3635307647488352 chr10 135534747 6479205 0.04780475223818435 0.4630202320579987 chr11 135006516 6265165 0.04640638974788446 0.366430047029691 chr12 133851895 9457178 0.07065404639956722 0.3341934674317423 chr13 115169878 5846271 0.05076215327761309 0.2849635587684346 chr14 107349540 1295987 0.012072590157349534 0.16506662523981563 chr15 102531392 3086009 0.030098186904553095 0.22366653316778604 chr16 90354753 4465376 0.049420488150745095 0.30136277779343523 chr17 81195210 3321390 0.04090623079859021 0.2741689783088834 chr18 78077248 4502108 0.057662227029313326 0.5524956630835924 chr19 59128983 1576496 0.026661984022285652 0.5423243220425451 chr20 63025520 3539330 0.056157093190187087 0.30177212678119025 chr21 48129895 2827157 0.05874014476865158 0.3112370880261758 chr22 51304566 1804755 0.03517727837323485 0.22850187034888658 chrMT 16571 108422 6.542876108864885 4.70586066096819 chrX 155270560 6118929 0.039408172418519 0.2769029553210598 chrY 59373566 448716 0.007557504630932897 0.20413822670336754