BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,659,294 number of mapped reads = 5,918,114 (88.87%) number of supplementary alignments = 56,373 (0.85%) number of secondary alignments = 0 number of mapped bases = 398,382,820 bp number of sequenced bases = 398,237,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 432,694 duplication rate = 5.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7285 >>>>>>> ACTG content number of A's = 111,543,998 bp (28.01%) number of C's = 70,473,112 bp (17.7%) number of T's = 129,089,416 bp (32.42%) number of G's = 86,346,770 bp (21.68%) number of N's = 783,763 bp (0.2%) GC percentage = 39.38% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,949,015 number of insertions = 32,051 mapped reads with insertion percentage = 0.54% number of deletions = 88,182 mapped reads with deletion percentage = 1.47% homopolymer indels = 49.27% >>>>>>> Coverage mean coverageData = 0.1287X std coverageData = 0.8595X There is a 8.6% of reference with a coverageData >= 1X There is a 2.61% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 31831876 0.127710317720733 1.130458922288421 chr2 243199373 26164582 0.10758490730154967 0.8076049045003498 chr3 198022430 35926187 0.18142483657028147 0.5950102866895635 chr4 191154276 24785564 0.12966261869025625 0.5447218850008745 chr5 180915260 22432661 0.12399540536270959 0.48745234257201087 chr6 171115067 32580220 0.19039948130342024 1.031193174265618 chr7 159138663 28124638 0.176730390150381 1.2905172567150114 chr8 146364022 29612749 0.20232259673760536 1.624527151599245 chr9 141213431 20002118 0.14164458620086923 1.0160352685902156 chr10 135534747 17017496 0.12555817881889728 0.7199662668782687 chr11 135006516 13809696 0.10228910729019924 0.6123732181132427 chr12 133851895 19326592 0.14438788483345716 0.554207445643205 chr13 115169878 10720823 0.09308703965111433 0.4187601802892036 chr14 107349540 10982440 0.10230542208192042 0.5878309864389173 chr15 102531392 9862893 0.0961938856735701 0.431759789581912 chr16 90354753 8915038 0.09866706182020109 0.5546573238983608 chr17 81195210 8095849 0.09970845570816309 0.46992774574537854 chr18 78077248 9923601 0.12709977943894743 1.758258706059677 chr19 59128983 7177248 0.12138290962995255 0.8915718633409757 chr20 63025520 6166768 0.09784557112737824 0.47921897033487115 chr21 48129895 9090987 0.18888441373080078 0.7313363638864602 chr22 51304566 3238217 0.06311752057312014 0.3406584025960862 chrMT 16571 202137 12.198237885462555 7.263978607165073 chrX 155270560 11530884 0.0742631700433102 0.43349489897291393 chrY 59373566 861556 0.014510767300047297 0.29263010715171567