BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525086.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 = 2,332,471 number of mapped reads = 1,613,358 (69.17%) number of supplementary alignments = 5,778 (0.25%) number of secondary alignments = 0 number of mapped bases = 93,246,710 bp number of sequenced bases = 93,218,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,365 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5697 >>>>>>> ACTG content number of A's = 24,454,105 bp (26.23%) number of C's = 16,383,974 bp (17.58%) number of T's = 29,374,055 bp (31.51%) number of G's = 22,997,237 bp (24.67%) number of N's = 8,832 bp (0.01%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 447,752 number of insertions = 6,524 mapped reads with insertion percentage = 0.4% number of deletions = 17,503 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.19% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2766X There is a 2.65% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7514474 0.030148265909435788 0.497669614347614 chr2 243199373 7846520 0.03226373449572997 0.36500790387209187 chr3 198022430 6176437 0.031190592904046275 0.19783044273726766 chr4 191154276 6031793 0.03155458055251665 0.2278785586448009 chr5 180915260 5565207 0.030761401774510342 0.19581605065084312 chr6 171115067 5281079 0.030862735190934413 0.21081250129125875 chr7 159138663 5149345 0.03235759873136549 0.31384151253203846 chr8 146364022 4740857 0.03239086310432218 0.2640845185258567 chr9 141213431 3936395 0.027875500029455415 0.22536701640275147 chr10 135534747 4559708 0.03364235445837369 0.3169204859637122 chr11 135006516 4185237 0.03100025927637448 0.22957690597335506 chr12 133851895 4197482 0.031359152591750754 0.20102780766153885 chr13 115169878 2898368 0.025166024748241898 0.17769142126320348 chr14 107349540 2780848 0.02590461030387275 0.18173614220946446 chr15 102531392 2782463 0.027137669212566627 0.18486359375470066 chr16 90354753 2755302 0.03049426741280561 0.21189953205415019 chr17 81195210 2514952 0.030974142440175965 0.20305160383131246 chr18 78077248 2468431 0.03161524084455436 0.3530848438153866 chr19 59128983 1912913 0.03235152886022071 0.36297038303236023 chr20 63025520 1999622 0.031727179720214924 0.20551398324585676 chr21 48129895 1251724 0.02600720404646634 0.20409611440696293 chr22 51304566 1170002 0.02280502674947099 0.1675992599520118 chrMT 16571 20887 1.2604550117675457 1.318309371144299 chrX 155270560 5197452 0.03347351874044893 0.2267822777430394 chrY 59373566 309212 0.0052079068318045775 0.16094980464561448