BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716446.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 = 743,370 number of mapped reads = 711,642 (95.73%) number of supplementary alignments = 14,331 (1.93%) number of secondary alignments = 0 number of mapped bases = 58,911,447 bp number of sequenced bases = 58,886,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,855 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8236 >>>>>>> ACTG content number of A's = 14,913,586 bp (25.33%) number of C's = 11,753,748 bp (19.96%) number of T's = 18,063,360 bp (30.67%) number of G's = 14,151,542 bp (24.03%) number of N's = 4,280 bp (0.01%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 414,360 number of insertions = 4,982 mapped reads with insertion percentage = 0.69% number of deletions = 14,217 mapped reads with deletion percentage = 1.97% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.221X There is a 1.73% of reference with a coverageData >= 1X There is a 0.12% 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 4669642 0.018734725639861095 0.34456147062472875 chr2 243199373 5040234 0.02072469981244565 0.24885136648545508 chr3 198022430 3922055 0.019806114893146196 0.14941355324103717 chr4 191154276 3766240 0.019702619678777157 0.1620338984300328 chr5 180915260 3457606 0.01911174325482549 0.14854854154211714 chr6 171115067 3278089 0.019157220094475957 0.15875109024789608 chr7 159138663 3450103 0.021679854128220242 0.2530226093288494 chr8 146364022 3117366 0.021298717795552244 0.3547597803940441 chr9 141213431 2512636 0.017793180026905515 0.23371595859139133 chr10 135534747 2805855 0.020702108220263252 0.2001478496537998 chr11 135006516 2680137 0.019851908481217307 0.22595064676350624 chr12 133851895 2734131 0.020426539347836652 0.1544491587432914 chr13 115169878 1805064 0.015673056456654403 0.1327356682521435 chr14 107349540 1739367 0.016202836081086143 0.1556382484359337 chr15 102531392 1721694 0.016791871898120724 0.13788436786835975 chr16 90354753 1704213 0.018861354200149272 0.15919960421158244 chr17 81195210 1586749 0.019542396651231028 0.16096604873492482 chr18 78077248 1578886 0.02022210106585724 0.41052268287482585 chr19 59128983 1175189 0.019875007828225287 0.2540006270550948 chr20 63025520 1265952 0.020086339628772598 0.1557778345311738 chr21 48129895 771288 0.016025133651340815 0.14412034555182202 chr22 51304566 707940 0.013798771828612682 0.12483253258703858 chrMT 16571 11835 0.7141995051596162 1.0624042532220543 chrX 155270560 3246782 0.020910480389843382 0.17948317665298597 chrY 59373566 162394 0.002735122899641905 0.10540053101269038