BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716569.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 = 1,061,586 number of mapped reads = 989,606 (93.22%) number of supplementary alignments = 25,086 (2.36%) number of secondary alignments = 0 number of mapped bases = 76,494,252 bp number of sequenced bases = 76,463,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,901 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0296 >>>>>>> ACTG content number of A's = 19,418,142 bp (25.4%) number of C's = 16,072,053 bp (21.02%) number of T's = 22,414,610 bp (29.31%) number of G's = 18,554,919 bp (24.27%) number of N's = 3,292 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 498,423 number of insertions = 6,916 mapped reads with insertion percentage = 0.69% number of deletions = 14,985 mapped reads with deletion percentage = 1.49% homopolymer indels = 38.97% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2316X There is a 2.19% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8617816 0.03457490282441463 0.40218691152352404 chr2 243199373 7366072 0.030288203086773584 0.2593191623855823 chr3 198022430 4957819 0.02503665367605074 0.17702753079791322 chr4 191154276 3817619 0.019971402575373203 0.20231085893077388 chr5 180915260 4796713 0.026513589843112185 0.1809408852016746 chr6 171115067 4779880 0.027933717841456943 0.19443749761546492 chr7 159138663 4788051 0.030087289347152553 0.3014553024064936 chr8 146364022 4766186 0.03256391792786345 0.2514659801977751 chr9 141213431 2337070 0.016549913017834685 0.16782781111113934 chr10 135534747 4266498 0.031478997780547004 0.3189547376397087 chr11 135006516 3291199 0.024378075203422032 0.2058930105442002 chr12 133851895 2742561 0.02048951940501104 0.15706102804614644 chr13 115169878 1532882 0.01330974753659112 0.12594220635202835 chr14 107349540 1507906 0.014046692701244924 0.1357515862118569 chr15 102531392 1593458 0.01554117201490837 0.13570521219064918 chr16 90354753 2266847 0.025088298343309067 0.18323408974557295 chr17 81195210 1469633 0.018099996292884765 0.16051319749288323 chr18 78077248 2154894 0.027599512728727325 0.25086526540433957 chr19 59128983 1960169 0.03315073083533333 0.2994710987123158 chr20 63025520 2078308 0.03297565811436383 0.20626822683391224 chr21 48129895 1189898 0.024722638601226952 0.1958859102129711 chr22 51304566 1224276 0.02386290530164508 0.17301096921303424 chrMT 16571 21339 1.287731579264981 1.5405605332295407 chrX 155270560 2734649 0.01761215390734728 0.15163131438940797 chrY 59373566 232509 0.003916035631075283 0.1600124767045869