BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716194.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 = 514,401 number of mapped reads = 479,567 (93.23%) number of supplementary alignments = 10,011 (1.95%) number of secondary alignments = 0 number of mapped bases = 36,860,927 bp number of sequenced bases = 36,846,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,441 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0919 >>>>>>> ACTG content number of A's = 9,127,279 bp (24.77%) number of C's = 7,449,545 bp (20.22%) number of T's = 11,120,753 bp (30.18%) number of G's = 9,147,250 bp (24.83%) number of N's = 1,314 bp (0%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 243,658 number of insertions = 3,679 mapped reads with insertion percentage = 0.75% number of deletions = 6,830 mapped reads with deletion percentage = 1.4% homopolymer indels = 38.5% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.1397X There is a 1.1% 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 4004184 0.016064890767112674 0.22186441862030082 chr2 243199373 3464302 0.014244699553563405 0.15226114071629884 chr3 198022430 2356361 0.011899465126248577 0.11555916257317947 chr4 191154276 1854866 0.009703502525886473 0.12875104067103574 chr5 180915260 1911918 0.010568030579620536 0.10853305386453435 chr6 171115067 2269203 0.013261269388977885 0.12435937269971561 chr7 159138663 2299836 0.014451774048145672 0.17027885167766632 chr8 146364022 2291405 0.015655520862907144 0.15188202472142612 chr9 141213431 1093262 0.007741912311442953 0.10667081284184532 chr10 135534747 1925296 0.01420518385591556 0.18667587718288273 chr11 135006516 1115608 0.008263364117921538 0.11001106636585915 chr12 133851895 1365343 0.010200400973030677 0.10641392045924375 chr13 115169878 695389 0.006037941622200903 0.08128551591187876 chr14 107349540 714294 0.006653908344646842 0.08647647603931913 chr15 102531392 769746 0.007507417825752332 0.0911513339462757 chr16 90354753 1121898 0.012416590857151698 0.12228732918884667 chr17 81195210 927951 0.011428642157585404 0.11661870348639572 chr18 78077248 1080661 0.013840920725074736 0.1522103745837586 chr19 59128983 928410 0.015701436975501505 0.1738511749484118 chr20 63025520 1011570 0.016050165075988266 0.1383076431477461 chr21 48129895 571344 0.0118708756792426 0.12781181449255719 chr22 51304566 602499 0.011743574636222437 0.11599962323576539 chrMT 16571 6485 0.39134632792227386 0.6837283287521543 chrX 155270560 2341756 0.015081777253846447 0.1325571052023244 chrY 59373566 137340 0.0023131506030815126 0.09672921282317008