BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975190.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 43,216,288 number of mapped reads = 43,107,837 (99.75%) number of supplementary alignments = 114,820 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,580,675 number of mapped paired reads (second in pair) = 21,527,162 number of mapped paired reads (both in pair) = 43,029,068 number of mapped paired reads (singletons) = 78,769 number of mapped bases = 4,198,620,965 bp number of sequenced bases = 4,197,082,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,009,794 duplication rate = 37.26% >>>>>>> Insert size mean insert size = 190,191.8459 std insert size = 4,376,077.5217 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 55.8232 >>>>>>> ACTG content number of A's = 1,121,217,064 bp (26.71%) number of C's = 947,793,851 bp (22.58%) number of T's = 1,133,856,746 bp (27.02%) number of G's = 993,897,803 bp (23.68%) number of N's = 317,114 bp (0.01%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 26,836,317 number of insertions = 323,382 mapped reads with insertion percentage = 0.74% number of deletions = 1,028,031 mapped reads with deletion percentage = 2.35% homopolymer indels = 50.09% >>>>>>> Coverage mean coverageData = 1.3563X std coverageData = 17.45X There is a 11.26% of reference with a coverageData >= 1X There is a 4.9% of reference with a coverageData >= 2X There is a 3.09% of reference with a coverageData >= 3X There is a 2.52% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 2.04% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.8% of reference with a coverageData >= 8X There is a 1.71% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.57% of reference with a coverageData >= 11X There is a 1.51% of reference with a coverageData >= 12X There is a 1.45% of reference with a coverageData >= 13X There is a 1.4% of reference with a coverageData >= 14X There is a 1.35% of reference with a coverageData >= 15X There is a 1.31% of reference with a coverageData >= 16X There is a 1.27% of reference with a coverageData >= 17X There is a 1.23% of reference with a coverageData >= 18X There is a 1.2% of reference with a coverageData >= 19X There is a 1.16% of reference with a coverageData >= 20X There is a 1.13% of reference with a coverageData >= 21X There is a 1.1% of reference with a coverageData >= 22X There is a 1.07% of reference with a coverageData >= 23X There is a 1.05% of reference with a coverageData >= 24X There is a 1.02% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.98% of reference with a coverageData >= 27X There is a 0.95% of reference with a coverageData >= 28X There is a 0.93% of reference with a coverageData >= 29X There is a 0.91% of reference with a coverageData >= 30X There is a 0.89% of reference with a coverageData >= 31X There is a 0.87% of reference with a coverageData >= 32X There is a 0.86% of reference with a coverageData >= 33X There is a 0.84% of reference with a coverageData >= 34X There is a 0.82% of reference with a coverageData >= 35X There is a 0.81% of reference with a coverageData >= 36X There is a 0.79% of reference with a coverageData >= 37X There is a 0.78% of reference with a coverageData >= 38X There is a 0.76% of reference with a coverageData >= 39X There is a 0.75% of reference with a coverageData >= 40X There is a 0.73% of reference with a coverageData >= 41X There is a 0.72% of reference with a coverageData >= 42X There is a 0.71% of reference with a coverageData >= 43X There is a 0.69% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.66% of reference with a coverageData >= 47X There is a 0.65% of reference with a coverageData >= 48X There is a 0.64% of reference with a coverageData >= 49X There is a 0.63% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 603203632 2.420068722717445 26.58868987091306 chr2 243199373 265156222 1.0902833289788127 13.381695147779762 chr3 198022430 308132795 1.5560499636329077 18.491992514913917 chr4 191154276 153254159 0.8017302160690353 11.293163131931975 chr5 180915260 293256026 1.6209579335651398 19.911583940093934 chr6 171115067 241644422 1.41217501320325 19.21233987623823 chr7 159138663 169085968 1.0625071545310143 13.754716443646466 chr8 146364022 174615841 1.1930243417333803 16.454139723310888 chr9 141213431 150213515 1.063733909276661 14.666290240360325 chr10 135534747 154566413 1.1404190912017564 14.462170402761673 chr11 135006516 215178641 1.5938389299669062 17.37321787138308 chr12 133851895 187788896 1.4029603092283454 16.02937533944517 chr13 115169878 53337704 0.4631219979237974 9.073102524644584 chr14 107349540 146221379 1.3621053150297617 17.65097526029803 chr15 102531392 132608179 1.2933422283001874 15.48639374579807 chr16 90354753 115873413 1.2824274224954164 14.85192596475104 chr17 81195210 138865342 1.7102651991416735 16.567230370288826 chr18 78077248 60254079 0.7717239086090739 10.936786045382004 chr19 59128983 179718334 3.0394288026229033 28.30684011216059 chr20 63025520 88657015 1.4066843875306383 17.39364917067415 chr21 48129895 34610727 0.7191107938215947 10.211592397682518 chr22 51304566 65332632 1.2734272423238118 15.203872689477947 chrMT 16571 63300 3.819926377406312 9.589765889955302 chrX 155270560 265549310 1.7102360550512603 23.930954301679133 chrY 59373566 1433021 0.024135673440938345 1.415793708824763