BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 665,886 number of mapped reads = 320,737 (48.17%) number of supplementary alignments = 11,842 (1.78%) number of secondary alignments = 0 number of mapped bases = 40,758,462 bp number of sequenced bases = 39,890,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 285,982 duplication rate = 41.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0121 >>>>>>> ACTG content number of A's = 10,225,790 bp (25.63%) number of C's = 7,687,199 bp (19.27%) number of T's = 9,656,256 bp (24.21%) number of G's = 12,320,368 bp (30.89%) number of N's = 484 bp (0%) GC percentage = 50.16% >>>>>>> Mismatches and indels general error rate = 0.0456 number of mismatches = 1,650,542 number of insertions = 48,315 mapped reads with insertion percentage = 14.24% number of deletions = 136,324 mapped reads with deletion percentage = 39.15% homopolymer indels = 32.2% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 6.1512X There is a 0.04% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 2432590 0.009759614600920091 1.6850549836265996 chr2 243199373 7386638 0.030372767449527924 20.054740294397288 chr3 198022430 2092037 0.0105646466412921 3.4117104695884466 chr4 191154276 1372057 0.007177746837324215 1.5850747294322842 chr5 180915260 2159655 0.011937384386480168 2.3115858968439147 chr6 171115067 1054295 0.006161321843154817 1.1123340858747668 chr7 159138663 1783773 0.01120892287501498 2.430265532189693 chr8 146364022 1857984 0.012694267174483631 3.0644139102768375 chr9 141213431 1312415 0.009293839762309861 2.660627341902237 chr10 135534747 2231618 0.016465283253157215 3.316452917650751 chr11 135006516 1409176 0.010437836941144382 1.356038885619111 chr12 133851895 1654071 0.012357471666725376 2.0809407192381757 chr13 115169878 1128577 0.00979923760968124 1.9005877872527157 chr14 107349540 1371336 0.012774493491075975 2.7659541382864132 chr15 102531392 999977 0.009752886218495892 1.7121103668039461 chr16 90354753 958208 0.010604954008340878 1.5739216491478634 chr17 81195210 1903993 0.023449572948946125 6.185873331317438 chr18 78077248 875529 0.011213625254824555 1.9087107090052198 chr19 59128983 553090 0.009353957601469317 1.2861819783134416 chr20 63025520 904394 0.014349647571333009 2.5051712239551422 chr21 48129895 142120 0.0029528425108760366 0.47212750796764763 chr22 51304566 741917 0.014461032571642843 4.0559542542369 chrMT 16571 569096 34.34288817814254 275.76323152983963 chrX 155270560 3599410 0.02318153550808344 2.7356330238425244 chrY 59373566 264506 0.004454945488704519 1.0950266981422196