BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234083.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,644,608 number of mapped reads = 1,427,343 (86.79%) number of supplementary alignments = 10,130 (0.62%) number of secondary alignments = 0 number of mapped bases = 94,289,991 bp number of sequenced bases = 94,236,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,205 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4562 >>>>>>> ACTG content number of A's = 26,166,005 bp (27.77%) number of C's = 17,545,491 bp (18.62%) number of T's = 29,119,516 bp (30.9%) number of G's = 21,388,084 bp (22.7%) number of N's = 17,327 bp (0.02%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 803,107 number of insertions = 7,934 mapped reads with insertion percentage = 0.55% number of deletions = 30,808 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.343X There is a 2.74% of reference with a coverageData >= 1X There is a 0.21% 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 8313426 0.03335368219604155 0.6821215215426187 chr2 243199373 6147820 0.025278930303821136 0.33749460068481424 chr3 198022430 10502406 0.05303644642680125 0.24842694007138835 chr4 191154276 3629725 0.018988458306839026 0.16761942128075208 chr5 180915260 5801386 0.03206686931771261 0.1957620359317153 chr6 171115067 5686760 0.03323354336763343 0.24566978422762464 chr7 159138663 6107049 0.03837564602387039 0.5040667784144384 chr8 146364022 5096856 0.03482314800012806 0.4874807643980989 chr9 141213431 3650863 0.025853511058732084 0.27393357145817204 chr10 135534747 4042004 0.029822640241472544 0.2951192983708849 chr11 135006516 3703189 0.027429705689168367 0.27955643248702317 chr12 133851895 3039635 0.022708942596591553 0.16705879629241754 chr13 115169878 4865893 0.04224970178400293 0.22141349094786708 chr14 107349540 4298879 0.040045621061813585 0.2396071297637431 chr15 102531392 1667886 0.016267076526182343 0.14326117902524624 chr16 90354753 2482357 0.02747345233736625 0.22224091224455553 chr17 81195210 2114709 0.026044750669405252 0.1999313909415827 chr18 78077248 2030365 0.02600456665685758 0.5942237047507816 chr19 59128983 2743553 0.04639946200326158 0.44570187341938783 chr20 63025520 1769836 0.0280812597817519 0.19575546611710792 chr21 48129895 1821440 0.0378442545947794 0.22225653136573106 chr22 51304566 929870 0.018124507670525855 0.1440561367092965 chrMT 16571 28897 1.7438295817995293 1.7228883556937757 chrX 155270560 3563085 0.022947589034263804 0.19437015028752533 chrY 59373566 252102 0.0042460309694048026 0.11031669000017218