BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472534.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 = 20,648,668 number of mapped reads = 20,387,537 (98.74%) number of supplementary alignments = 69,141 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,228,466 number of mapped paired reads (second in pair) = 10,159,071 number of mapped paired reads (both in pair) = 20,254,894 number of mapped paired reads (singletons) = 132,643 number of mapped bases = 2,008,875,104 bp number of sequenced bases = 2,008,618,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,179,533 duplication rate = 46.45% >>>>>>> Insert size mean insert size = 22,393.4791 std insert size = 1,447,911.5722 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 54.8927 >>>>>>> ACTG content number of A's = 558,789,799 bp (27.82%) number of C's = 448,098,369 bp (22.31%) number of T's = 556,239,077 bp (27.69%) number of G's = 445,181,695 bp (22.16%) number of N's = 309,421 bp (0.02%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 12,322,190 number of insertions = 110,342 mapped reads with insertion percentage = 0.54% number of deletions = 103,301 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.6489X std coverageData = 22.3566X There is a 6.14% of reference with a coverageData >= 1X There is a 2.7% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 216766662 0.8696735082557728 30.828832383025198 chr2 243199373 133803509 0.5501803205717969 23.562696248766766 chr3 198022430 226980540 1.1462365147220948 26.742978668498573 chr4 191154276 85418617 0.4468569512931011 16.908627320601564 chr5 180915260 157213043 0.8689871877032375 37.697294232459605 chr6 171115067 130704887 0.7638420700849213 23.08031404180252 chr7 159138663 87265389 0.5483607022637862 18.680381730667726 chr8 146364022 117768522 0.8046275333975176 23.27911122794515 chr9 141213431 116474208 0.824809702414213 22.15459692213176 chr10 135534747 49352724 0.36413336869253166 13.897909484892988 chr11 135006516 72906120 0.5400192684033117 15.887608086823706 chr12 133851895 94223570 0.7039390066162305 20.38102241955224 chr13 115169878 46582712 0.4044695784083404 16.39795172353512 chr14 107349540 66367710 0.6182393515612643 22.451873266891376 chr15 102531392 40794089 0.397869259397161 11.852000673879195 chr16 90354753 69444775 0.7685791028613624 22.04902687009974 chr17 81195210 62979206 0.7756517410325067 16.898303354896083 chr18 78077248 34835222 0.4461635481824359 13.737614763694587 chr19 59128983 30730637 0.5197220625289631 15.916089186579534 chr20 63025520 38512732 0.611065676253048 15.762141809001212 chr21 48129895 13991628 0.29070555836450507 16.153067768876905 chr22 51304566 16254080 0.31681546628812723 9.047151731717792 chrMT 16571 4822 0.29099028423148876 0.7847455189457964 chrX 155270560 94653162 0.6096014724233622 22.75874917071228 chrY 59373566 4846538 0.08162787459995244 5.064008202092701