BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716365.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 = 746,071 number of mapped reads = 627,803 (84.15%) number of supplementary alignments = 1,626 (0.22%) number of secondary alignments = 0 number of mapped bases = 34,887,135 bp number of sequenced bases = 34,877,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,171 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9525 >>>>>>> ACTG content number of A's = 8,324,253 bp (23.87%) number of C's = 6,932,302 bp (19.88%) number of T's = 10,833,670 bp (31.06%) number of G's = 8,786,375 bp (25.19%) number of N's = 919 bp (0%) GC percentage = 45.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 185,077 number of insertions = 2,349 mapped reads with insertion percentage = 0.37% number of deletions = 5,908 mapped reads with deletion percentage = 0.93% homopolymer indels = 37.88% >>>>>>> Coverage mean coverageData = 0.0113X std coverageData = 0.1261X There is a 1.06% of reference with a coverageData >= 1X There is a 0.05% 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 3413714 0.013695909708485741 0.14866006023161696 chr2 243199373 3007946 0.012368230900003184 0.16280862984937527 chr3 198022430 2367970 0.011958089798211244 0.11898487998818406 chr4 191154276 2246848 0.011754107975068264 0.1225547694167879 chr5 180915260 2153944 0.011905817121231232 0.11503263102407255 chr6 171115067 1512839 0.008841062488085869 0.1018612088624031 chr7 159138663 2014607 0.012659444047233199 0.13709545731080044 chr8 146364022 2183293 0.014916869392944121 0.1352520112214975 chr9 141213431 1526616 0.010810699727280191 0.11655376320529752 chr10 135534747 1797667 0.013263513894337369 0.1679232687715127 chr11 135006516 1467204 0.010867653232381761 0.12649147060792443 chr12 133851895 1645901 0.012296434054967992 0.11738413533171316 chr13 115169878 611337 0.005308132739360895 0.07709891850034278 chr14 107349540 1113610 0.010373682085642846 0.11010307491500512 chr15 102531392 687776 0.006707955354785391 0.08649117650061026 chr16 90354753 938396 0.010385684967784706 0.11395557879679953 chr17 81195210 1366920 0.01683498324593286 0.14096584439309984 chr18 78077248 943796 0.012087977281166467 0.13642279301153468 chr19 59128983 934845 0.01581026685339743 0.15150044888767253 chr20 63025520 872885 0.013849707229706316 0.12640576445837365 chr21 48129895 464369 0.0096482446097171 0.10792712905433768 chr22 51304566 369890 0.007209689679472194 0.0912895456440111 chrMT 16571 1264 0.07627783477158892 0.2701741567978531 chrX 155270560 1139344 0.007337797970201176 0.09537872646972143 chrY 59373566 104154 0.0017542149986409777 0.061733012044549285