BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237786.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 = 2,688,920 number of mapped reads = 685,028 (25.48%) number of supplementary alignments = 2,836 (0.11%) number of secondary alignments = 0 number of mapped bases = 40,032,817 bp number of sequenced bases = 40,015,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,770 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.0738 >>>>>>> ACTG content number of A's = 11,122,090 bp (27.79%) number of C's = 7,944,753 bp (19.85%) number of T's = 11,728,366 bp (29.31%) number of G's = 9,186,399 bp (22.96%) number of N's = 33,831 bp (0.08%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 306,747 number of insertions = 2,805 mapped reads with insertion percentage = 0.41% number of deletions = 10,348 mapped reads with deletion percentage = 1.5% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1398X There is a 1.16% of reference with a coverageData >= 1X There is a 0.1% 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 3422752 0.013732170400490195 0.13769812447142613 chr2 243199373 597116 0.002455253040475561 0.09717964984031817 chr3 198022430 5198149 0.02625030406908955 0.17585848735268683 chr4 191154276 427352 0.0022356392383291496 0.06711441860320543 chr5 180915260 2304765 0.012739472612758039 0.12152777671606725 chr6 171115067 2919958 0.01706429510383209 0.1477260089158543 chr7 159138663 347637 0.0021844911440534096 0.07095898542667084 chr8 146364022 2873023 0.01962929797050808 0.15837656766459757 chr9 141213431 2101236 0.014879859409407028 0.13977361667454932 chr10 135534747 3467314 0.025582472958023083 0.2331930301823412 chr11 135006516 5401595 0.04000988367109629 0.2520783289334059 chr12 133851895 5889174 0.043997688639372645 0.23001876745763133 chr13 115169878 170040 0.0014764277166291694 0.04025644435215527 chr14 107349540 889932 0.008290040180889456 0.09938388564297372 chr15 102531392 159336 0.0015540216210075447 0.041623768899569764 chr16 90354753 1528320 0.01691466081479964 0.1442585960047047 chr17 81195210 178467 0.002197999118420902 0.06190414901694128 chr18 78077248 386080 0.004944846416717967 0.1178455335040495 chr19 59128983 296410 0.005012939255187258 0.10828726046158207 chr20 63025520 375657 0.00596039509075054 0.08464083157950562 chr21 48129895 91306 0.001897074572882405 0.05970847807703572 chr22 51304566 415088 0.00809066389919369 0.09645785127391773 chrMT 16571 154242 9.307947619334982 6.063764328314592 chrX 155270560 366566 0.0023608210081808166 0.0661035420283797 chrY 59373566 71302 0.001200904793220606 0.0559492933196873