BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716314.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 = 3,120,572 number of mapped reads = 2,929,715 (93.88%) number of supplementary alignments = 60,508 (1.94%) number of secondary alignments = 0 number of mapped bases = 232,055,453 bp number of sequenced bases = 231,954,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,295 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4248 >>>>>>> ACTG content number of A's = 59,532,540 bp (25.67%) number of C's = 45,858,175 bp (19.77%) number of T's = 70,709,881 bp (30.48%) number of G's = 55,837,495 bp (24.07%) number of N's = 16,561 bp (0.01%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,465,735 number of insertions = 19,411 mapped reads with insertion percentage = 0.65% number of deletions = 52,461 mapped reads with deletion percentage = 1.76% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.075X std coverageData = 0.6325X There is a 5.87% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 22629719 0.09079102354573472 1.323683529563843 chr2 243199373 19274270 0.07925295925824612 0.7124892603978765 chr3 198022430 14423494 0.07283767803475596 0.3244022192789407 chr4 191154276 14508427 0.07589904502057804 0.46141915649153437 chr5 180915260 13381218 0.07396400944840142 0.33348888499633905 chr6 171115067 12804670 0.07483075701334939 0.37483998873181834 chr7 159138663 12559025 0.0789187540176833 0.7909214190924038 chr8 146364022 11324826 0.07737438371295918 0.7093663508265383 chr9 141213431 9360085 0.0662832489354359 0.5053424178560718 chr10 135534747 10588372 0.07812293330211477 0.6078263311223542 chr11 135006516 12841563 0.09511809785536574 0.7219291045499057 chr12 133851895 9991453 0.07464558495791188 0.3335215231189055 chr13 115169878 8060930 0.06999165181020683 0.32402688893321047 chr14 107349540 6733770 0.0627275161123187 0.33366225846074193 chr15 102531392 6494979 0.0633462481422275 0.30402670493429995 chr16 90354753 5236960 0.057959983577178284 0.33912595790336675 chr17 81195210 7470484 0.09200646195754651 0.48482052664452896 chr18 78077248 6054804 0.07754889106747205 0.9047165453695056 chr19 59128983 4500134 0.076107075949539 0.85792594143462 chr20 63025520 4924687 0.07813798283615907 0.36492461882132776 chr21 48129895 2971232 0.0617336065245935 0.3905623272687803 chr22 51304566 2648612 0.051625268596951 0.27702737323999166 chrMT 16571 73954 4.462856798020638 3.2948654763977347 chrX 155270560 12512286 0.08058376294900978 0.4246832608830852 chrY 59373566 685499 0.011545525158451827 0.3833547873912333