BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524842.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 = 1,891,140 number of mapped reads = 1,746,434 (92.35%) number of supplementary alignments = 8,414 (0.44%) number of secondary alignments = 0 number of mapped bases = 102,302,614 bp number of sequenced bases = 102,272,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,289 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1443 >>>>>>> ACTG content number of A's = 26,250,092 bp (25.67%) number of C's = 19,503,625 bp (19.07%) number of T's = 32,343,828 bp (31.63%) number of G's = 24,161,372 bp (23.62%) number of N's = 13,837 bp (0.01%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 488,710 number of insertions = 6,706 mapped reads with insertion percentage = 0.38% number of deletions = 19,050 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3315X There is a 2.97% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8507773 0.034133407434920694 0.6559477086415472 chr2 243199373 6599549 0.02713637341491008 0.32331238700163495 chr3 198022430 7356784 0.03715126614697133 0.20765479991395192 chr4 191154276 5539358 0.028978467633127915 0.1939741190670517 chr5 180915260 6227276 0.034420954871358 0.20229331366315145 chr6 171115067 6731779 0.03934065607442973 0.23888509004288527 chr7 159138663 4699867 0.029533156251287596 0.4513728802236672 chr8 146364022 11029784 0.07535857411734695 0.43153111539092015 chr9 141213431 4167005 0.029508559989594757 0.2690923510391962 chr10 135534747 5066499 0.037381550577579935 0.29258641312604683 chr11 135006516 4843543 0.03587636466376186 0.28499716124752034 chr12 133851895 4063214 0.03035604389463444 0.19348374692763243 chr13 115169878 2698295 0.02342882572125326 0.1680791039041951 chr14 107349540 2124817 0.019793442990067772 0.16531607977487484 chr15 102531392 2993345 0.029194424669470986 0.18477621966909222 chr16 90354753 2894353 0.03203321246420761 0.20952017869238693 chr17 81195210 2715519 0.03344432510242907 0.23133892512593515 chr18 78077248 2470404 0.03164051069013088 0.4891991252918639 chr19 59128983 1446916 0.024470503746022488 0.4308622761882528 chr20 63025520 2135715 0.0338865113687281 0.2019517157892164 chr21 48129895 1529105 0.0317703788882149 0.20515885029552142 chr22 51304566 588376 0.011468296993292956 0.11402842161694603 chrMT 16571 432782 26.11683060768813 14.635366454579614 chrX 155270560 5186644 0.03340391121150075 0.2306570774072376 chrY 59373566 253912 0.004276515916190717 0.10328514376707112