BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472746.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 = 19,425,874 number of mapped reads = 19,221,695 (98.95%) number of supplementary alignments = 89,895 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,653,502 number of mapped paired reads (second in pair) = 9,568,193 number of mapped paired reads (both in pair) = 19,095,084 number of mapped paired reads (singletons) = 126,611 number of mapped bases = 1,897,466,438 bp number of sequenced bases = 1,897,203,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,678,188 duplication rate = 47.61% >>>>>>> Insert size mean insert size = 27,110.3265 std insert size = 1,616,196.0587 median insert size = 260 >>>>>>> Mapping quality mean mapping quality = 55.401 >>>>>>> ACTG content number of A's = 521,189,284 bp (27.47%) number of C's = 430,366,540 bp (22.68%) number of T's = 518,674,011 bp (27.34%) number of G's = 426,608,946 bp (22.49%) number of N's = 364,219 bp (0.02%) GC percentage = 45.17% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 12,700,433 number of insertions = 117,103 mapped reads with insertion percentage = 0.6% number of deletions = 105,445 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.6129X std coverageData = 22.1326X There is a 5.07% of reference with a coverageData >= 1X There is a 2.16% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179724853 0.7210608032948491 24.966613144749886 chr2 243199373 134606350 0.5534814845102417 20.04565102724686 chr3 198022430 165859937 0.8375815658862483 19.841922813841062 chr4 191154276 65240159 0.3412958389693569 16.184004506260724 chr5 180915260 108401777 0.599185369990348 19.782452480445176 chr6 171115067 126772014 0.7408582787160408 25.116595565316835 chr7 159138663 64575716 0.4057826978224644 13.077363406416652 chr8 146364022 78725058 0.5378716499058764 16.00264468375342 chr9 141213431 117956335 0.8353053542052951 25.90889608895759 chr10 135534747 58802483 0.43385540831090347 17.447440791390772 chr11 135006516 84621569 0.6267961836745717 20.33599959260876 chr12 133851895 79947439 0.5972828326412563 20.112491713455093 chr13 115169878 49292755 0.42800040996830785 19.627761053206335 chr14 107349540 101382533 0.9444151600463309 48.41898959178118 chr15 102531392 52935973 0.5162903962134836 17.618532544804726 chr16 90354753 75964135 0.8407320309978602 24.29951242567509 chr17 81195210 89225240 1.098897829071444 25.960567334749243 chr18 78077248 32878715 0.4211049421209108 16.89571170106797 chr19 59128983 51675849 0.8739512566958915 25.13890090139565 chr20 63025520 57580858 0.9136117877329691 25.686790834125798 chr21 48129895 5701087 0.11845209718408901 3.5592628890038718 chr22 51304566 25311833 0.4933641383887742 16.59351479364177 chrMT 16571 3335 0.20125520487598816 0.6948960842920548 chrX 155270560 87137853 0.561200094853783 24.547664513742173 chrY 59373566 3142582 0.05292897516042745 1.9276167645853028