BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716547.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 = 1,000,988 number of mapped reads = 756,707 (75.6%) number of supplementary alignments = 864 (0.09%) number of secondary alignments = 0 number of mapped bases = 39,860,079 bp number of sequenced bases = 39,849,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,107 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6748 >>>>>>> ACTG content number of A's = 8,302,256 bp (20.83%) number of C's = 6,985,728 bp (17.53%) number of T's = 13,310,416 bp (33.4%) number of G's = 11,250,700 bp (28.23%) number of N's = 711 bp (0%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 276,368 number of insertions = 2,787 mapped reads with insertion percentage = 0.37% number of deletions = 6,040 mapped reads with deletion percentage = 0.79% homopolymer indels = 38.34% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1416X 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 3773426 0.015139083645452583 0.15964655115606646 chr2 243199373 3499292 0.014388573279751014 0.21290573643965596 chr3 198022430 2786343 0.014070845408775158 0.13092508881318135 chr4 191154276 2510063 0.013131084757947031 0.13081606608012683 chr5 180915260 2433175 0.013449252429010135 0.12698133413036922 chr6 171115067 1758736 0.010278089655307793 0.12950544910259915 chr7 159138663 2231533 0.014022569738442505 0.15239892639615438 chr8 146364022 2451914 0.01675216331510759 0.1459783232216491 chr9 141213431 1755628 0.012432443483368093 0.12919810520381622 chr10 135534747 1937559 0.014295662499004776 0.15178368022936564 chr11 135006516 1741298 0.01289788116597276 0.13452390450372687 chr12 133851895 1962404 0.01466101021580606 0.13436853251694406 chr13 115169878 710149 0.0061661001325363915 0.08688627924662644 chr14 107349540 1280642 0.011929645902534841 0.12152399151095016 chr15 102531392 733837 0.007157193379370096 0.09390637009873122 chr16 90354753 1069486 0.011836521759956557 0.12832866591009984 chr17 81195210 1586981 0.019545253962641392 0.16024881738068494 chr18 78077248 1088074 0.013935865157542438 0.1487304581788535 chr19 59128983 1077213 0.018218020086697585 0.1663508285889523 chr20 63025520 1070785 0.016989705122623343 0.14770615631135992 chr21 48129895 545492 0.011333745897430277 0.12241632835015183 chr22 51304566 460906 0.008983722813287224 0.10548782184399559 chrMT 16571 52127 3.1456761812805505 2.942813602967745 chrX 155270560 1226170 0.007896989616061152 0.1002894823311902 chrY 59373566 116846 0.0019679801614071826 0.06671879635861837