BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695922.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 = 2,113,204 number of mapped reads = 2,070,193 (97.96%) number of supplementary alignments = 61,058 (2.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,037,079 number of mapped paired reads (second in pair) = 1,033,114 number of mapped paired reads (both in pair) = 2,065,188 number of mapped paired reads (singletons) = 5,005 number of mapped bases = 308,765,831 bp number of sequenced bases = 308,682,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,051 duplication rate = 0.62% >>>>>>> Insert size mean insert size = 35,134.3215 std insert size = 1,737,584.7542 median insert size = 295 >>>>>>> Mapping quality mean mapping quality = 55.1626 >>>>>>> ACTG content number of A's = 91,007,462 bp (29.48%) number of C's = 63,248,978 bp (20.49%) number of T's = 90,746,564 bp (29.4%) number of G's = 63,639,181 bp (20.62%) number of N's = 40,677 bp (0.01%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,068,883 number of insertions = 27,460 mapped reads with insertion percentage = 1.29% number of deletions = 34,565 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.72% >>>>>>> Coverage mean coverageData = 0.0997X std coverageData = 0.5137X There is a 7.09% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 25125860 0.10080560641812804 0.45014214357171756 chr2 243199373 27209251 0.11188043235621335 0.5114034745238286 chr3 198022430 23212064 0.11721936752316392 0.47796468825597754 chr4 191154276 19458323 0.10179381496022616 0.4379967765425859 chr5 180915260 21558691 0.11916458014652827 0.5011371166947474 chr6 171115067 18761862 0.1096447105969926 0.4933102849073774 chr7 159138663 17890563 0.11242122223937498 1.0709588926641358 chr8 146364022 18119676 0.12379870238876053 0.551678685290915 chr9 141213431 12308150 0.087159910447895 0.3978239347596356 chr10 135534747 13385565 0.09876113171185541 0.4526625780610237 chr11 135006516 13398042 0.09923996557321722 0.44808013150502607 chr12 133851895 14398379 0.10756948192627382 0.4714052204351988 chr13 115169878 9835149 0.08539688650186814 0.391004800778967 chr14 107349540 10682236 0.0995089126604548 0.44635917812084175 chr15 102531392 9596280 0.09359357961315887 0.4196452508892729 chr16 90354753 10154011 0.11237937864762909 0.5441374539606444 chr17 81195210 6713260 0.08268049309805345 0.3874021167030903 chr18 78077248 8399094 0.10757415527760404 0.4316237134927944 chr19 59128983 4366931 0.07385432284536333 0.7145853481266228 chr20 63025520 6404999 0.10162548440695135 0.5015001475863291 chr21 48129895 4559675 0.09473685741471076 0.5416363991629339 chr22 51304566 3635109 0.07085351818393708 0.41418097572293466 chrMT 16571 7943 0.4793313620179832 0.8604124806188767 chrX 155270560 8118471 0.05228596457692946 0.3254094600844962 chrY 59373566 1466247 0.024695282745860338 0.20945442620789995