BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038393.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,514,274 number of mapped reads = 14,996,746 (96.66%) number of supplementary alignments = 294,095 (1.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,554,908 number of mapped paired reads (second in pair) = 7,441,838 number of mapped paired reads (both in pair) = 14,863,038 number of mapped paired reads (singletons) = 133,708 number of mapped bases = 2,156,240,711 bp number of sequenced bases = 2,154,644,331 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,592,445 duplication rate = 10.46% >>>>>>> Insert size mean insert size = 73,625.7132 std insert size = 2,516,867.5928 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 53.7457 >>>>>>> ACTG content number of A's = 633,488,470 bp (29.4%) number of C's = 439,626,954 bp (20.4%) number of T's = 630,088,050 bp (29.24%) number of G's = 451,393,366 bp (20.95%) number of N's = 47,491 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 29,422,480 number of insertions = 407,547 mapped reads with insertion percentage = 2.56% number of deletions = 759,592 mapped reads with deletion percentage = 4.87% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.6965X std coverageData = 12.7564X There is a 28.05% of reference with a coverageData >= 1X There is a 15.71% of reference with a coverageData >= 2X There is a 8.1% of reference with a coverageData >= 3X There is a 4.78% of reference with a coverageData >= 4X There is a 2.69% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 144716672 0.5806070669729645 21.091411169164626 chr2 243199373 189091991 0.7775184149015055 11.258554584792899 chr3 198022430 118568533 0.5987631451649189 1.4815144256032915 chr4 191154276 126776937 0.6632178973595129 11.889533158021752 chr5 180915260 119273103 0.65927607765094 1.551350183020862 chr6 171115067 172515809 1.008185965295505 19.970834241932522 chr7 159138663 118455773 0.7443557132310455 8.894298675679629 chr8 146364022 100738738 0.6882752784697321 2.914910898502438 chr9 141213431 81810920 0.5793423431514811 17.308878091525134 chr10 135534747 107064415 0.7899407153502858 28.330991505062173 chr11 135006516 96390112 0.713966368852893 9.84929299373672 chr12 133851895 74571811 0.5571218173638857 1.3431197899767935 chr13 115169878 149032095 1.2940197349171456 2.242733690466104 chr14 107349540 40465136 0.3769474559462481 1.3664427918392217 chr15 102531392 43018343 0.4195626545282834 1.0801512800771573 chr16 90354753 93237959 1.0319098431933071 16.882995336512685 chr17 81195210 66911619 0.8240833295461641 11.713992903859957 chr18 78077248 33590408 0.43022018399009143 16.472077301356098 chr19 59128983 34939575 0.5909043793295075 11.217850516332742 chr20 63025520 67634134 1.0731229825632538 4.1872917924488195 chr21 48129895 19655443 0.40838325119969615 5.0976486262932985 chr22 51304566 13564651 0.26439461548120297 0.9051393848655919 chrMT 16571 1895741 114.4011224428218 80.9252848047509 chrX 155270560 104816320 0.6750559797040727 2.8097400522327955 chrY 59373566 37504473 0.6316695379219769 16.993761699805784