BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524479.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 = 1,533,543 number of mapped reads = 1,410,338 (91.97%) number of supplementary alignments = 3,096 (0.2%) number of secondary alignments = 0 number of mapped bases = 81,767,753 bp number of sequenced bases = 81,742,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,806 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1306 >>>>>>> ACTG content number of A's = 20,811,525 bp (25.46%) number of C's = 15,837,951 bp (19.38%) number of T's = 25,605,817 bp (31.33%) number of G's = 19,485,310 bp (23.84%) number of N's = 1,643 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 381,700 number of insertions = 6,017 mapped reads with insertion percentage = 0.43% number of deletions = 15,070 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2491X There is a 2.35% of reference with a coverageData >= 1X There is a 0.21% 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 8088800 0.03245247681850309 0.4311171985831221 chr2 243199373 6419335 0.02639535999132695 0.2812665958514833 chr3 198022430 4503865 0.022744216400132047 0.16774597039496827 chr4 191154276 4642857 0.024288533310131134 0.19392851064110064 chr5 180915260 4455170 0.02462572808949339 0.17250553429784982 chr6 171115067 3543689 0.02070939200228347 0.20168604117009675 chr7 159138663 4088933 0.025694152023886238 0.32240659120245946 chr8 146364022 7503655 0.05126707299694183 0.28316293848293655 chr9 141213431 3483878 0.024671010224232848 0.22725481412626994 chr10 135534747 4292341 0.03166967213212122 0.25943122032561355 chr11 135006516 2759631 0.02044072450547498 0.24218637046475783 chr12 133851895 3778625 0.028229895437789657 0.18515334652963467 chr13 115169878 1839109 0.015968663264538666 0.14052358943167814 chr14 107349540 1935900 0.018033612440258244 0.15041578858119145 chr15 102531392 2148870 0.02095816664617213 0.1688841842942722 chr16 90354753 2556959 0.028299108957776688 0.19727843411573007 chr17 81195210 2855740 0.035171286582053304 0.21500320550251342 chr18 78077248 1938650 0.024829896668489136 0.35471885763976846 chr19 59128983 1655452 0.027997302101407696 0.3116607673064115 chr20 63025520 2285395 0.0362614223571658 0.2154441879930949 chr21 48129895 1117435 0.02321706706403577 0.17886418706659418 chr22 51304566 666305 0.012987245618645327 0.12447373714427211 chrMT 16571 16538 0.9980085691871341 1.3276949578937847 chrX 155270560 4924861 0.031717931589864815 0.21630293839373588 chrY 59373566 265760 0.004476065998798186 0.12594385329369462