BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716406.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 = 979,944 number of mapped reads = 878,051 (89.6%) number of supplementary alignments = 4,787 (0.49%) number of secondary alignments = 0 number of mapped bases = 50,118,114 bp number of sequenced bases = 50,104,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,690 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9228 >>>>>>> ACTG content number of A's = 12,672,576 bp (25.29%) number of C's = 9,618,271 bp (19.2%) number of T's = 15,823,208 bp (31.58%) number of G's = 11,989,242 bp (23.93%) number of N's = 1,111 bp (0%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 245,695 number of insertions = 3,288 mapped reads with insertion percentage = 0.37% number of deletions = 8,077 mapped reads with deletion percentage = 0.91% homopolymer indels = 40.21% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.155X There is a 1.51% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5590076 0.02242753088266127 0.21764550809240324 chr2 243199373 4177687 0.01717803359632839 0.1737779468977901 chr3 198022430 3369852 0.017017526751893712 0.13783695935669577 chr4 191154276 3223837 0.01686510533512732 0.1438934657386271 chr5 180915260 2524693 0.013955113570850795 0.12487546583729457 chr6 171115067 2589571 0.015133506624521849 0.13414716873827773 chr7 159138663 2157516 0.013557459635060526 0.1377821215108306 chr8 146364022 3195410 0.021831936266413887 0.16804851618062597 chr9 141213431 1812540 0.012835464637921021 0.14967800272117268 chr10 135534747 2388095 0.01761979900253918 0.17266593529440125 chr11 135006516 1575048 0.011666459121128642 0.1361208758159506 chr12 133851895 2217025 0.016563269425509442 0.13658839939626313 chr13 115169878 1578765 0.01370814163752088 0.12266931130011272 chr14 107349540 1757426 0.01637106223277715 0.13999736402876783 chr15 102531392 1421788 0.013866855528499993 0.12430230842044919 chr16 90354753 1474474 0.016318720942106943 0.1435140191564502 chr17 81195210 1116497 0.013750774214390233 0.12476040977167825 chr18 78077248 1216615 0.015582196237244427 0.24532701052866424 chr19 59128983 955052 0.016152011273388552 0.17716693635294145 chr20 63025520 1590272 0.02523219165823622 0.17014400364380453 chr21 48129895 642509 0.013349478530962928 0.1282985117051252 chr22 51304566 587841 0.01145786907153644 0.11285018201391299 chrMT 16571 840 0.05069096614567618 0.22209979707840197 chrX 155270560 2803475 0.01805541887657261 0.15156300296009453 chrY 59373566 151210 0.002546756245026617 0.06738693601481408