BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230387.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 = 1,698,301 number of mapped reads = 1,090,574 (64.22%) number of supplementary alignments = 5,344 (0.31%) number of secondary alignments = 0 number of mapped bases = 66,842,588 bp number of sequenced bases = 66,805,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,841 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6092 >>>>>>> ACTG content number of A's = 16,864,062 bp (25.24%) number of C's = 11,071,572 bp (16.57%) number of T's = 22,930,788 bp (34.32%) number of G's = 15,832,560 bp (23.7%) number of N's = 106,961 bp (0.16%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 763,183 number of insertions = 5,586 mapped reads with insertion percentage = 0.51% number of deletions = 23,668 mapped reads with deletion percentage = 2.14% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2275X There is a 1.61% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 6274925 0.02517516295375649 0.33758747795073685 chr2 243199373 5719595 0.023518132178737154 0.24670219894482467 chr3 198022430 4335929 0.021896150855233925 0.1910181678356261 chr4 191154276 4505172 0.02356825122761052 0.20256193076304613 chr5 180915260 4357586 0.024086337437759533 0.20111532959283165 chr6 171115067 3847374 0.022484133439868274 0.22190939796633696 chr7 159138663 3645375 0.022906909806072708 0.259045002216088 chr8 146364022 3777059 0.025805925174699013 0.29746834090644975 chr9 141213431 2743543 0.019428343186421126 0.20996538099887155 chr10 135534747 3004640 0.02216878008412116 0.21981924458263113 chr11 135006516 3062183 0.022681742264943714 0.21212471219094978 chr12 133851895 3081006 0.023018023017156386 0.1971047180886947 chr13 115169878 1914531 0.01662353935983157 0.16584472288120827 chr14 107349540 1785898 0.016636289265887866 0.1706365030658709 chr15 102531392 1832857 0.017876056925083005 0.1742962258479533 chr16 90354753 1701715 0.01883370761912215 0.18068901474975668 chr17 81195210 1665870 0.02051685068614269 0.19183087731114068 chr18 78077248 1497967 0.019185704393679448 0.2912560774499703 chr19 59128983 1162496 0.019660341528282332 0.240326700778983 chr20 63025520 1356591 0.021524471356999513 0.19394168655585822 chr21 48129895 847027 0.017598770992540085 0.1752421850899865 chr22 51304566 699411 0.013632529315227031 0.148044846640355 chrMT 16571 92862 5.603886307404502 5.299363962338172 chrX 155270560 3753487 0.024173848538963212 0.20861338764875345 chrY 59373566 177489 0.0029893606188316196 0.07788723727502084