BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716426.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 = 1,583,676 number of mapped reads = 1,456,243 (91.95%) number of supplementary alignments = 5,217 (0.33%) number of secondary alignments = 0 number of mapped bases = 84,581,382 bp number of sequenced bases = 84,554,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,116 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5978 >>>>>>> ACTG content number of A's = 20,662,719 bp (24.44%) number of C's = 15,021,854 bp (17.77%) number of T's = 28,095,632 bp (33.23%) number of G's = 20,772,900 bp (24.57%) number of N's = 1,599 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 430,181 number of insertions = 6,313 mapped reads with insertion percentage = 0.43% number of deletions = 16,390 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.26% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2672X There is a 2.46% of reference with a coverageData >= 1X There is a 0.19% 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% 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 7196624 0.028873043409588937 0.4066984973566061 chr2 243199373 6723658 0.02764669134241559 0.4052348504139036 chr3 198022430 4866297 0.02457447370987216 0.17124422520076746 chr4 191154276 5239106 0.02740773635636589 0.22693490404750608 chr5 180915260 4810855 0.026591759036799882 0.1771265580147849 chr6 171115067 4459653 0.02606230461283693 0.20655750252384558 chr7 159138663 4717495 0.029643927572773437 0.32047456321827256 chr8 146364022 4461377 0.030481377452171957 0.33615875411145485 chr9 141213431 2787240 0.019737782590949157 0.18772889718050034 chr10 135534747 3734770 0.0275558119424534 0.29782908266096864 chr11 135006516 3000737 0.02222660867716933 0.20483342083004374 chr12 133851895 4193615 0.03133026245164478 0.1942839944621674 chr13 115169878 2524649 0.021921087734416114 0.16183944582251578 chr14 107349540 2806601 0.026144508863289027 0.17803473076580714 chr15 102531392 3109378 0.03032610734476325 0.19007436355586205 chr16 90354753 2880414 0.03187894277127845 0.20118262664132383 chr17 81195210 3657177 0.04504178263717774 0.24061877094585518 chr18 78077248 1597166 0.02045622817033715 0.32250554483398164 chr19 59128983 2189433 0.03702808485645694 0.3264350833229705 chr20 63025520 2817180 0.044699036199939327 0.24017725147249347 chr21 48129895 1082399 0.022489120327397347 0.21045251594962433 chr22 51304566 789297 0.015384537118976896 0.13517693688837507 chrMT 16571 76546 4.619274636413011 3.2295728797476553 chrX 155270560 4524246 0.02913782239208772 0.19912267850251852 chrY 59373566 335469 0.005650140670344779 0.26696248437609005