BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068145.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 = 3,268,914 number of mapped reads = 3,067,152 (93.83%) number of supplementary alignments = 26,173 (0.8%) number of secondary alignments = 0 number of mapped bases = 197,604,218 bp number of sequenced bases = 197,519,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 306,615 duplication rate = 8.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2349 >>>>>>> ACTG content number of A's = 52,446,359 bp (26.55%) number of C's = 35,215,922 bp (17.83%) number of T's = 64,442,449 bp (32.63%) number of G's = 45,391,636 bp (22.98%) number of N's = 22,687 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,116,703 number of insertions = 12,778 mapped reads with insertion percentage = 0.41% number of deletions = 49,064 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.0638X std coverageData = 0.6478X There is a 5.06% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.2% 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 20394387 0.08182281319170716 1.468377003734093 chr2 243199373 18572907 0.07636905790871426 0.8348965342649528 chr3 198022430 13118591 0.06624800533959714 0.31324151749811135 chr4 191154276 10491516 0.05488507094656883 0.30241590843446303 chr5 180915260 9167997 0.05067564228689166 0.2741851977511387 chr6 171115067 11187003 0.06537707751942148 0.391067558459665 chr7 159138663 18377915 0.1154836584243516 0.9816944540776978 chr8 146364022 7576514 0.05176486609530312 0.7275102577960876 chr9 141213431 7842405 0.05553582930790769 0.47374401170546143 chr10 135534747 9748130 0.07192347509233185 0.4535915083689055 chr11 135006516 10051937 0.07445519888832625 0.4170136614478769 chr12 133851895 7948567 0.05938329823421626 0.31495353443382673 chr13 115169878 4198867 0.03645803115290267 0.2511959740274765 chr14 107349540 4212655 0.039242413148673015 0.28719113756829645 chr15 102531392 3938102 0.03840874412394596 0.26967132479125944 chr16 90354753 4076487 0.045116464432147806 0.2796122827485895 chr17 81195210 5126411 0.06313686484707658 0.32691480855955807 chr18 78077248 5180341 0.06634891895779933 0.8472456507196605 chr19 59128983 4006606 0.06776044160948955 0.8939171626152386 chr20 63025520 2981381 0.04730434592209632 0.27944231987415535 chr21 48129895 3484377 0.07239527532731996 0.34113599146014206 chr22 51304566 2216938 0.04321131963186279 0.24884175194396735 chrMT 16571 98558 5.947619334982801 4.1378608301597435 chrX 155270560 13052139 0.08406061651352323 0.4111703862246927 chrY 59373566 553487 0.009322111459500343 0.24406414276434615