BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004060.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 = 3,052,550 number of mapped reads = 2,750,879 (90.12%) number of supplementary alignments = 37,490 (1.23%) number of secondary alignments = 0 number of mapped bases = 180,600,114 bp number of sequenced bases = 180,498,223 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,158 duplication rate = 5.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2189 >>>>>>> ACTG content number of A's = 50,832,819 bp (28.16%) number of C's = 33,095,625 bp (18.34%) number of T's = 57,283,766 bp (31.74%) number of G's = 39,148,167 bp (21.69%) number of N's = 137,846 bp (0.08%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,584,626 number of insertions = 12,792 mapped reads with insertion percentage = 0.46% number of deletions = 60,812 mapped reads with deletion percentage = 2.18% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.0583X std coverageData = 0.5021X There is a 4.42% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% 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 15963897 0.06404757162069417 0.9339600348833894 chr2 243199373 14068928 0.05784935966919619 0.4859243254431776 chr3 198022430 10887905 0.05498319054058674 0.2924804861495949 chr4 191154276 11437142 0.05983199664338139 0.310677838600052 chr5 180915260 7865314 0.0434751275265558 0.26419429323410293 chr6 171115067 11156364 0.06519802256805357 0.36946148543823953 chr7 159138663 12673033 0.07963516069002037 0.8406816130201581 chr8 146364022 12147055 0.0829920825761402 0.7154904794582033 chr9 141213431 5343762 0.03784174042198578 0.42067563682366255 chr10 135534747 7164598 0.05286170637851266 0.38475603048169055 chr11 135006516 7720847 0.05718869895138987 0.4275313889572065 chr12 133851895 8867246 0.0662466975159373 0.33376704160239107 chr13 115169878 5770549 0.05010467233454914 0.2802095083053057 chr14 107349540 5219459 0.048621158507060204 0.31456279766424433 chr15 102531392 5967831 0.058204915427267384 0.302221577005323 chr16 90354753 3305899 0.036587992222168984 0.272951690615245 chr17 81195210 3914058 0.048205528380307165 0.2964577223702137 chr18 78077248 4851793 0.062140932528769455 0.8173344362348063 chr19 59128983 2984507 0.05047451940785114 0.6104925587643387 chr20 63025520 4602561 0.07302694210218337 0.3531695610832071 chr21 48129895 2047471 0.04254052496894082 0.2761086250813152 chr22 51304566 1651209 0.032184445337672285 0.2193762189735311 chrMT 16571 8250 0.4978577032164625 0.9088792636305693 chrX 155270560 14535780 0.0936158148717954 0.4354292361469874 chrY 59373566 444656 0.007489124032065044 0.12888771873560795