BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524799.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 = 1,169,784 number of mapped reads = 1,069,057 (91.39%) number of supplementary alignments = 3,720 (0.32%) number of secondary alignments = 0 number of mapped bases = 61,409,893 bp number of sequenced bases = 61,389,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,627 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5775 >>>>>>> ACTG content number of A's = 14,788,299 bp (24.09%) number of C's = 11,934,321 bp (19.44%) number of T's = 19,281,873 bp (31.41%) number of G's = 15,378,337 bp (25.05%) number of N's = 6,978 bp (0.01%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 308,214 number of insertions = 3,754 mapped reads with insertion percentage = 0.35% number of deletions = 12,138 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.1905X There is a 1.81% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4922058 0.01974742522306494 0.243116474951814 chr2 243199373 5144652 0.021154051248314692 0.29672103773711955 chr3 198022430 4026042 0.020331242273918162 0.1539113973187863 chr4 191154276 3916513 0.020488754329513404 0.16998818888752076 chr5 180915260 3646980 0.02015849851471899 0.1526998349915311 chr6 171115067 3456521 0.02019998040266086 0.16464067825619585 chr7 159138663 3342678 0.021004813896168022 0.22014740173274638 chr8 146364022 3063009 0.020927335544250074 0.17801401601856243 chr9 141213431 2636540 0.018670603648175646 0.1667470243091109 chr10 135534747 2987475 0.022042133593977935 0.22329486754380568 chr11 135006516 2770791 0.020523387182289778 0.17186091309130302 chr12 133851895 2758192 0.020606297729292514 0.1555818451097809 chr13 115169878 1901228 0.016508031726837465 0.13864977149434787 chr14 107349540 1817302 0.01692882894514499 0.1427010537186706 chr15 102531392 1811461 0.017667379371968342 0.14351644599397065 chr16 90354753 1878656 0.02079199973021895 0.1704830180520848 chr17 81195210 1771501 0.021817801813678418 0.16275540156131343 chr18 78077248 1610159 0.0206226402856822 0.23736338183773578 chr19 59128983 1366468 0.02310995269443413 0.20533397507127635 chr20 63025520 1347628 0.02138225912297114 0.16088168981134288 chr21 48129895 832169 0.017290064730039408 0.15532397754351757 chr22 51304566 792894 0.015454647837777245 0.13499386667687738 chrMT 16571 14496 0.8747812443425261 1.0903297941791716 chrX 155270560 3390110 0.0218335658736595 0.16657674395615366 chrY 59373566 204370 0.003442104184882545 0.10091897416182662