BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004149.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 = 3,286,238 number of mapped reads = 2,625,408 (79.89%) number of supplementary alignments = 11,626 (0.35%) number of secondary alignments = 0 number of mapped bases = 164,671,796 bp number of sequenced bases = 164,587,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 233,053 duplication rate = 7.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3299 >>>>>>> ACTG content number of A's = 42,270,757 bp (25.68%) number of C's = 28,428,007 bp (17.27%) number of T's = 54,868,094 bp (33.34%) number of G's = 39,004,172 bp (23.7%) number of N's = 16,493 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,670,258 number of insertions = 14,690 mapped reads with insertion percentage = 0.56% number of deletions = 50,896 mapped reads with deletion percentage = 1.92% homopolymer indels = 49.46% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.5335X There is a 3.91% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17978075 0.07212850635184576 0.8329424213700549 chr2 243199373 17016187 0.06996805456402225 0.8729678030223886 chr3 198022430 12059208 0.060898192189642354 0.32027315726393313 chr4 191154276 8570902 0.04483761587420623 0.2845628146931763 chr5 180915260 8907676 0.04923673105298027 0.2937048265378053 chr6 171115067 11060768 0.06463935756165762 0.4273370534968998 chr7 159138663 8413920 0.05287162680259542 0.5879011637433744 chr8 146364022 10463854 0.07149198182050504 0.5807560642135216 chr9 141213431 5816212 0.04118738535571733 0.5661001536597114 chr10 135534747 6690890 0.049366602646921234 0.39588036812676236 chr11 135006516 6381026 0.04726457795562993 0.4690500441654515 chr12 133851895 6046641 0.04517411576429307 0.2954012912426901 chr13 115169878 3032701 0.026332414800335206 0.20916760249942243 chr14 107349540 3274145 0.03049985123364292 0.3322106965439806 chr15 102531392 3498718 0.03412338340242177 0.24911122362966437 chr16 90354753 6043174 0.06688274605764237 0.3669334749856474 chr17 81195210 3779208 0.04654471612303238 0.34543488140870426 chr18 78077248 5757888 0.07374604186868881 1.1835097320207253 chr19 59128983 3331661 0.05634565032177198 0.7064046409476804 chr20 63025520 3405695 0.05403676161656421 0.35160984361837616 chr21 48129895 3618944 0.07519118834562179 0.37945563097672713 chr22 51304566 2424742 0.04726171935651887 0.2789898926493038 chrMT 16571 117828 7.11049423691992 8.653852803172041 chrX 155270560 6641477 0.042773575364190096 0.37272448234361194 chrY 59373566 340256 0.0057307657754631074 0.12141001386117521