BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231790.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 = 12,404,768 number of mapped reads = 6,463,020 (52.1%) number of supplementary alignments = 69,594 (0.56%) number of secondary alignments = 0 number of mapped bases = 406,246,371 bp number of sequenced bases = 406,097,081 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,464,692 duplication rate = 12.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.4807 >>>>>>> ACTG content number of A's = 120,535,302 bp (29.68%) number of C's = 79,390,886 bp (19.55%) number of T's = 118,626,859 bp (29.21%) number of G's = 87,512,742 bp (21.55%) number of N's = 31,292 bp (0.01%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,658,338 number of insertions = 30,343 mapped reads with insertion percentage = 0.47% number of deletions = 93,968 mapped reads with deletion percentage = 1.44% homopolymer indels = 44.31% >>>>>>> Coverage mean coverageData = 0.1312X std coverageData = 9.4484X There is a 3.81% of reference with a coverageData >= 1X There is a 2.39% of reference with a coverageData >= 2X There is a 1.7% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 9882166 0.03964750803970916 0.6068210971749091 chr2 243199373 28579240 0.11751362533323637 33.04694610613444 chr3 198022430 13675180 0.06905874248689908 0.6681087081464564 chr4 191154276 6425334 0.033613341717765186 0.5260939187707796 chr5 180915260 3548905 0.019616393885181382 0.4406038305482423 chr6 171115067 41747162 0.24397128044837804 1.2642888465982658 chr7 159138663 52347402 0.3289420748746645 4.864718796480069 chr8 146364022 63864358 0.43633918450259584 3.59357631214834 chr9 141213431 25602581 0.18130414946153386 1.9591487780837702 chr10 135534747 2302293 0.016986736250003846 0.4267251183338322 chr11 135006516 51976260 0.3849907511130796 3.1730741436363705 chr12 133851895 14514410 0.10843634301927514 1.0522605824827278 chr13 115169878 8424891 0.07315186180886638 0.696425448765086 chr14 107349540 13065869 0.12171332080230618 1.4239976217779093 chr15 102531392 5132894 0.05006168257229942 0.5641419876941847 chr16 90354753 1435194 0.015883990076316183 0.8857534078340651 chr17 81195210 4708314 0.05798758325768232 1.098725732099434 chr18 78077248 30017530 0.3844593754124121 4.5086431883903835 chr19 59128983 2250345 0.03805823956079204 0.7653145714692752 chr20 63025520 3738930 0.05932406428380123 0.6168488979638452 chr21 48129895 4416036 0.09175245447761729 1.0812225548382157 chr22 51304566 10110621 0.19707058822015958 1.1150715053713551 chrMT 16571 43846 2.645947740027759 3.58744885380261 chrX 155270560 7492663 0.04825552892963096 1.1106335012543567 chrY 59373566 943947 0.01589843870923973 0.37662568392734846