BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525123.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 = 834,511 number of mapped reads = 771,272 (92.42%) number of supplementary alignments = 18,025 (2.16%) number of secondary alignments = 0 number of mapped bases = 60,067,469 bp number of sequenced bases = 60,043,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,891 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5614 >>>>>>> ACTG content number of A's = 15,536,549 bp (25.88%) number of C's = 11,854,424 bp (19.74%) number of T's = 18,434,276 bp (30.7%) number of G's = 14,216,453 bp (23.68%) number of N's = 2,189 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 432,845 number of insertions = 4,480 mapped reads with insertion percentage = 0.57% number of deletions = 13,823 mapped reads with deletion percentage = 1.77% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.2285X There is a 1.79% of reference with a coverageData >= 1X There is a 0.1% 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 6080931 0.024396853960095048 0.39662875234734474 chr2 243199373 5264067 0.021645068139217613 0.2991455404965553 chr3 198022430 4033607 0.02036944501691046 0.14962703226850516 chr4 191154276 3971950 0.02077876615221519 0.15454453181818617 chr5 180915260 3741434 0.02068058824888514 0.15314296778170233 chr6 171115067 3467810 0.020265953552763415 0.16428596171566662 chr7 159138663 3417577 0.021475466335921147 0.33758887902033113 chr8 146364022 3150704 0.02152649235069531 0.28255694490584043 chr9 141213431 1433847 0.01015375796654923 0.174407793477921 chr10 135534747 2851682 0.021040228156400366 0.22577347172583231 chr11 135006516 2915173 0.021592831860056297 0.23243296276119732 chr12 133851895 2744160 0.02050146544432561 0.15095283625702624 chr13 115169878 2178079 0.018911880761044133 0.14499608914141407 chr14 107349540 1003058 0.009343850006250608 0.11023235261809536 chr15 102531392 1734569 0.01691744319632372 0.1366700491445561 chr16 90354753 1353885 0.014984103824621158 0.1358238297630572 chr17 81195210 1681925 0.02071458402533844 0.16595366878609696 chr18 78077248 1651458 0.021151590793773878 0.31967806275846433 chr19 59128983 1126125 0.019045228631786208 0.2883500651057677 chr20 63025520 1190960 0.018896472413079655 0.14728644268342822 chr21 48129895 790104 0.016416075705130876 0.13952899753341635 chr22 51304566 617375 0.012033529335381182 0.1152684674166229 chrMT 16571 13899 0.8387544505461348 1.2488157903198331 chrX 155270560 3526102 0.022709404796376082 0.19035171501329332 chrY 59373566 126988 0.002138796918480524 0.060308693269716294