BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695963.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 97,221,376 number of mapped reads = 96,693,322 (99.46%) number of supplementary alignments = 945,091 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 48,444,617 number of mapped paired reads (second in pair) = 48,248,705 number of mapped paired reads (both in pair) = 96,355,760 number of mapped paired reads (singletons) = 337,562 number of mapped bases = 9,599,327,089 bp number of sequenced bases = 9,597,049,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,207,101 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 73,588.2119 std insert size = 2,624,324.8217 median insert size = 337 >>>>>>> Mapping quality mean mapping quality = 54.0843 >>>>>>> ACTG content number of A's = 2,777,972,302 bp (28.95%) number of C's = 1,999,205,734 bp (20.83%) number of T's = 2,764,922,916 bp (28.81%) number of G's = 2,054,794,081 bp (21.41%) number of N's = 154,275 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 32,381,962 number of insertions = 974,168 mapped reads with insertion percentage = 0.99% number of deletions = 984,640 mapped reads with deletion percentage = 1% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 3.1009X std coverageData = 4.51X There is a 81.81% of reference with a coverageData >= 1X There is a 65.53% of reference with a coverageData >= 2X There is a 48.79% of reference with a coverageData >= 3X There is a 34.63% of reference with a coverageData >= 4X There is a 23.91% of reference with a coverageData >= 5X There is a 16.27% of reference with a coverageData >= 6X There is a 11.02% of reference with a coverageData >= 7X There is a 7.49% of reference with a coverageData >= 8X There is a 5.12% of reference with a coverageData >= 9X There is a 3.54% of reference with a coverageData >= 10X There is a 2.48% of reference with a coverageData >= 11X There is a 1.76% of reference with a coverageData >= 12X There is a 1.27% of reference with a coverageData >= 13X There is a 0.93% of reference with a coverageData >= 14X There is a 0.7% of reference with a coverageData >= 15X There is a 0.53% of reference with a coverageData >= 16X There is a 0.41% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 828183179 3.3226925400518863 6.515125006818442 chr2 243199373 849938953 3.494823783941252 4.955227491438263 chr3 198022430 644398329 3.254168373754428 2.8716999602232884 chr4 191154276 569843794 2.9810674703400304 4.254902542307692 chr5 180915260 572520187 3.1645765371036143 2.8454363675863688 chr6 171115067 567418557 3.3160058137954618 3.6999755309281492 chr7 159138663 501388413 3.1506385912014356 3.3431873726614656 chr8 146364022 486461637 3.323642178950234 3.2479456908511777 chr9 141213431 400006700 2.832639198462645 4.234724183834865 chr10 135534747 451976744 3.3347665746555752 5.267737022669172 chr11 135006516 470716731 3.4866223123630564 3.5167892229099253 chr12 133851895 466361381 3.484159719965115 3.3315549145961394 chr13 115169878 288993662 2.5092816543575744 2.8595007094758635 chr14 107349540 303766997 2.8297000341128618 3.1078160543148132 chr15 102531392 304305158 2.967921843877824 3.2611380658655413 chr16 90354753 297096997 3.2881169737689393 4.475586072481678 chr17 81195210 295319425 3.6371532877370476 5.28465614440478 chr18 78077248 252186077 3.229956017404712 7.053681747051915 chr19 59128983 210691576 3.563253844565532 5.418232962453512 chr20 63025520 227672354 3.6123835868391088 3.6356782634131357 chr21 48129895 119226623 2.4771843570404632 6.164209989993369 chr22 51304566 126698504 2.4695366100553313 3.3154760409674098 chrMT 16571 9309717 561.8077967533643 167.02456356927632 chrX 155270560 298381343 1.9216865257650904 2.2481156430403875 chrY 59373566 56464051 0.9509964585923641 5.133506462992302