BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472535.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,818,502 number of mapped reads = 19,621,576 (99.01%) number of supplementary alignments = 101,866 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,842,595 number of mapped paired reads (second in pair) = 9,778,981 number of mapped paired reads (both in pair) = 19,510,384 number of mapped paired reads (singletons) = 111,192 number of mapped bases = 1,930,606,141 bp number of sequenced bases = 1,930,333,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,150,906 duplication rate = 45.22% >>>>>>> Insert size mean insert size = 40,727.2538 std insert size = 1,977,542.1322 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.8605 >>>>>>> ACTG content number of A's = 548,375,567 bp (28.41%) number of C's = 420,247,769 bp (21.77%) number of T's = 543,599,582 bp (28.16%) number of G's = 417,813,618 bp (21.64%) number of N's = 296,683 bp (0.02%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,889,885 number of insertions = 120,614 mapped reads with insertion percentage = 0.61% number of deletions = 117,545 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.6236X std coverageData = 24.5252X There is a 5.77% of reference with a coverageData >= 1X There is a 2.64% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169835739 0.6813854196977106 25.310011571943665 chr2 243199373 138934038 0.5712763001243428 25.64543626405498 chr3 198022430 264978077 1.338121529970115 35.946512756282175 chr4 191154276 55771799 0.29176328234478 12.987431210538897 chr5 180915260 56008899 0.30958637209486917 10.646252454956748 chr6 171115067 177187148 1.0354853672821225 38.099647933689305 chr7 159138663 116968973 0.7350129176339756 30.084181710406952 chr8 146364022 126902837 0.8670357323195177 34.27646728351992 chr9 141213431 155707641 1.102640449264348 36.19462204969638 chr10 135534747 41753904 0.3080678934679385 20.667561867752948 chr11 135006516 76601156 0.567388584414696 20.143943331820964 chr12 133851895 63595372 0.47511745724630944 17.12563292631436 chr13 115169878 37865338 0.32877813763074404 11.66133387786246 chr14 107349540 29539242 0.27516878041582665 13.483864892348636 chr15 102531392 43872713 0.4278954195803759 15.396588033897741 chr16 90354753 87189664 0.9649704205378106 29.345605794776635 chr17 81195210 51121304 0.6296098501377113 18.34505174270333 chr18 78077248 39987310 0.5121506075623977 21.381821414854784 chr19 59128983 30657281 0.5184814526574895 18.096450015659432 chr20 63025520 37360200 0.5927789251084322 21.943212827666795 chr21 48129895 6590353 0.13692847241823403 3.786141402197614 chr22 51304566 16558929 0.3227574130536452 14.092036000958855 chrMT 16571 12758 0.7698992215315913 1.358237344976375 chrX 155270560 99538814 0.6410668835096621 21.23884993451275 chrY 59373566 6066652 0.10217765933075336 4.517454866850588