BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231775.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 854,957 number of mapped reads = 517,559 (60.54%) number of supplementary alignments = 4,215 (0.49%) number of secondary alignments = 0 number of mapped bases = 33,720,413 bp number of sequenced bases = 33,697,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,824 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8325 >>>>>>> ACTG content number of A's = 9,661,707 bp (28.67%) number of C's = 5,679,308 bp (16.85%) number of T's = 11,175,537 bp (33.16%) number of G's = 7,179,334 bp (21.31%) number of N's = 1,275 bp (0%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 320,843 number of insertions = 2,965 mapped reads with insertion percentage = 0.57% number of deletions = 13,204 mapped reads with deletion percentage = 2.51% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 0.1639X There is a 0.95% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% 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 2721944 0.010920510404666153 0.18797204753729307 chr2 243199373 3125745 0.012852603036932994 0.14611861375842142 chr3 198022430 2076992 0.010488670399610791 0.11528037708114856 chr4 191154276 2576343 0.013477820396756388 0.13358244754408763 chr5 180915260 2537857 0.014027876918729797 0.13340156401657413 chr6 171115067 2427991 0.014189229753800698 0.13859384351857326 chr7 159138663 320746 0.002015512723014394 0.05725902720108876 chr8 146364022 1958629 0.013381902008678061 0.46627951527626527 chr9 141213431 1754967 0.012427762625497003 0.13469654899720385 chr10 135534747 1969248 0.014529469701227243 0.15114219119334726 chr11 135006516 826487 0.0061218304455764195 0.09508968542819432 chr12 133851895 1882973 0.014067585669967542 0.13432779625237268 chr13 115169878 649727 0.005641466425795815 0.08553777279553275 chr14 107349540 1015343 0.009458289248374982 0.11031982253722769 chr15 102531392 1064137 0.010378645790744752 0.11524656883068621 chr16 90354753 948935 0.010502325206953971 0.11622188261171995 chr17 81195210 740414 0.009118936942216173 0.10760143325153852 chr18 78077248 542759 0.0069515641739831815 0.18464685587504967 chr19 59128983 583024 0.009860206795709644 0.1452369456553292 chr20 63025520 699182 0.0110936331822411 0.11849497331266984 chr21 48129895 479140 0.009955143263869577 0.11348119448482283 chr22 51304566 382760 0.007460544544904638 0.09638756750368203 chrMT 16571 20604 1.2433769838875144 1.4624893996871875 chrX 155270560 2315293 0.014911345718080749 0.14145139502091286 chrY 59373566 99173 0.0016703224461875846 0.05296796409738312