BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716205.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,472,017 number of mapped reads = 2,279,433 (92.21%) number of supplementary alignments = 56,471 (2.28%) number of secondary alignments = 0 number of mapped bases = 168,485,325 bp number of sequenced bases = 168,427,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,705 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0057 >>>>>>> ACTG content number of A's = 43,966,749 bp (26.1%) number of C's = 34,483,275 bp (20.47%) number of T's = 49,108,375 bp (29.16%) number of G's = 40,848,948 bp (24.25%) number of N's = 20,084 bp (0.01%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,230,071 number of insertions = 13,516 mapped reads with insertion percentage = 0.59% number of deletions = 33,898 mapped reads with deletion percentage = 1.47% homopolymer indels = 40.15% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.4091X There is a 4.51% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 15976709 0.06409897369924707 0.4775936639368373 chr2 243199373 13992781 0.057536254421182244 0.5970208212177849 chr3 198022430 10988294 0.05549014826249733 0.2759529442978712 chr4 191154276 10403700 0.05442567238202927 0.29459732843464137 chr5 180915260 10138287 0.056038871458383335 0.2804401434637121 chr6 171115067 9570976 0.055932982219502624 0.3200755437590302 chr7 159138663 9053970 0.05689359096852536 0.4956334069736283 chr8 146364022 8492425 0.05802262662609804 0.5182785181406004 chr9 141213431 6990385 0.04950226724538688 0.4488600145997523 chr10 135534747 7925489 0.058475698486381504 0.4323806447296968 chr11 135006516 7386531 0.0547124036590945 0.45673411258968827 chr12 133851895 7626316 0.05697577908777459 0.28305759423003507 chr13 115169878 5227687 0.04539109609892962 0.24675339872549426 chr14 107349540 5082169 0.04734225223508177 0.30438994866845104 chr15 102531392 4787077 0.04668889114467499 0.25590772141676005 chr16 90354753 4962644 0.05492399497788456 0.31524207434036455 chr17 81195210 4569251 0.056274883703115 0.3129270017356216 chr18 78077248 4559914 0.05840259636200292 0.8281408619995161 chr19 59128983 3400996 0.05751825631771817 0.4296528499011908 chr20 63025520 3528894 0.0559915094710841 0.2899749892042976 chr21 48129895 2195293 0.04561183854650005 0.2767917878412727 chr22 51304566 1933793 0.03769241513513631 0.22739343392129635 chrMT 16571 5884 0.3550781485728079 0.7171334594563903 chrX 155270560 9290241 0.05983259801471702 0.3721067087186178 chrY 59373566 395619 0.006663217769335263 0.1674380528905994