BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716906.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 = 788,172 number of mapped reads = 656,805 (83.33%) number of supplementary alignments = 1,823 (0.23%) number of secondary alignments = 0 number of mapped bases = 36,252,340 bp number of sequenced bases = 36,241,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,076 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2774 >>>>>>> ACTG content number of A's = 8,121,966 bp (22.41%) number of C's = 7,247,606 bp (20%) number of T's = 11,324,146 bp (31.25%) number of G's = 9,546,625 bp (26.34%) number of N's = 1,084 bp (0%) GC percentage = 46.34% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 196,337 number of insertions = 2,635 mapped reads with insertion percentage = 0.4% number of deletions = 6,531 mapped reads with deletion percentage = 0.98% homopolymer indels = 36.32% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 0.1307X There is a 1.09% of reference with a coverageData >= 1X There is a 0.06% 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 3539138 0.014199114071615492 0.15437088165208374 chr2 243199373 3190370 0.013118331518066866 0.16703037161579526 chr3 198022430 2374404 0.01199058106700337 0.12063632783003446 chr4 191154276 2358780 0.012339666416878899 0.12827855321445283 chr5 180915260 2188960 0.012099366300001448 0.1164732205348859 chr6 171115067 1575723 0.009208557888125656 0.10449727755252848 chr7 159138663 2079482 0.013067107394260313 0.14077849247244936 chr8 146364022 2230743 0.01524106108535334 0.13635323359999965 chr9 141213431 1565781 0.01108804586725182 0.11890520259095497 chr10 135534747 1861312 0.013733098273315847 0.1823973284319715 chr11 135006516 1516562 0.011233250401039903 0.131490787594204 chr12 133851895 1733938 0.01295415354410933 0.12105566760108781 chr13 115169878 653785 0.0056767013333121705 0.08149107998993851 chr14 107349540 1151308 0.010724852663551237 0.11203321989418517 chr15 102531392 739015 0.007207694985746414 0.09230845533040015 chr16 90354753 977164 0.01081474928053868 0.11833786506043262 chr17 81195210 1481675 0.01824830553427967 0.14972811490132426 chr18 78077248 944685 0.012099363440678646 0.13921629571252267 chr19 59128983 1008598 0.01705759086030619 0.1596429839318506 chr20 63025520 891827 0.014150252151826753 0.12879394276971745 chr21 48129895 506662 0.010526970815124362 0.11708131173030135 chr22 51304566 411415 0.008019071830760638 0.09684023883293584 chrMT 16571 14318 0.8640395872307043 1.1331243815937142 chrX 155270560 1138656 0.007333366995005364 0.09955488237151351 chrY 59373566 118039 0.001988073278266628 0.06934234943281728