BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237243.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 = 2,805,844 number of mapped reads = 2,508,911 (89.42%) number of supplementary alignments = 16,632 (0.59%) number of secondary alignments = 0 number of mapped bases = 168,503,537 bp number of sequenced bases = 168,434,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,128 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1148 >>>>>>> ACTG content number of A's = 46,679,029 bp (27.71%) number of C's = 30,667,913 bp (18.21%) number of T's = 53,759,085 bp (31.92%) number of G's = 37,325,863 bp (22.16%) number of N's = 2,672 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,335,865 number of insertions = 13,614 mapped reads with insertion percentage = 0.54% number of deletions = 41,732 mapped reads with deletion percentage = 1.65% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.4841X There is a 4.44% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13051669 0.052363636839243825 0.6712544989640735 chr2 243199373 13813056 0.056797251693572415 0.6475709262185892 chr3 198022430 13103951 0.06617407432077266 0.30088987511101745 chr4 191154276 7688162 0.04021967052413727 0.29494649929313377 chr5 180915260 10749071 0.05941494929725663 0.2896114944309325 chr6 171115067 18465458 0.10791251947439555 0.7497373559356554 chr7 159138663 9063907 0.05695603336820795 0.5705197105212501 chr8 146364022 8133345 0.055569291475196 0.6850281152867995 chr9 141213431 8316201 0.058891005912886575 0.5309577261255671 chr10 135534747 7037120 0.051921150522382276 0.448269953316812 chr11 135006516 3987264 0.029533863387749375 0.3166145263034713 chr12 133851895 6771389 0.050588667422302835 0.27819361420044214 chr13 115169878 4780217 0.041505791991895656 0.24025768548724943 chr14 107349540 6319334 0.05886689407332346 0.32169987637873615 chr15 102531392 3532205 0.03444998581507603 0.23860359489971172 chr16 90354753 5132031 0.056798683296716 0.317073368184857 chr17 81195210 4973385 0.061252197019996624 0.3674995835774233 chr18 78077248 5549321 0.0710747515076351 0.9104975762225896 chr19 59128983 2269307 0.03837892831676134 0.5162815052478937 chr20 63025520 2939745 0.04664372463725805 0.2686179410858756 chr21 48129895 2953855 0.06137256272842482 0.33778125634700656 chr22 51304566 1450262 0.02826769843448242 0.19294417590786742 chrMT 16571 44886 2.708707983827168 2.5042300224149376 chrX 155270560 7975957 0.051368121555045596 0.307229397131987 chrY 59373566 402439 0.0067780837014236265 0.17731027577325142