BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173948.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 9,612,588 number of mapped reads = 9,380,006 (97.58%) number of supplementary alignments = 1,359,792 (14.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,695,683 number of mapped paired reads (second in pair) = 4,684,323 number of mapped paired reads (both in pair) = 9,233,324 number of mapped paired reads (singletons) = 146,682 number of mapped bases = 1,060,890,775 bp number of sequenced bases = 1,060,204,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,813,623 duplication rate = 66.75% >>>>>>> Insert size mean insert size = 1,134,119.0278 std insert size = 10,344,255.4931 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.1648 >>>>>>> ACTG content number of A's = 315,383,650 bp (29.75%) number of C's = 210,923,513 bp (19.89%) number of T's = 313,341,231 bp (29.55%) number of G's = 220,547,808 bp (20.8%) number of N's = 8,050 bp (0%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 9,850,244 number of insertions = 134,615 mapped reads with insertion percentage = 1.38% number of deletions = 292,597 mapped reads with deletion percentage = 3.04% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.3427X std coverageData = 6.5336X There is a 6.78% of reference with a coverageData >= 1X There is a 5.26% of reference with a coverageData >= 2X There is a 4.05% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 2.51% of reference with a coverageData >= 5X There is a 2.06% of reference with a coverageData >= 6X There is a 1.56% of reference with a coverageData >= 7X There is a 1.33% of reference with a coverageData >= 8X There is a 1.02% of reference with a coverageData >= 9X There is a 0.9% of reference with a coverageData >= 10X There is a 0.69% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.48% of reference with a coverageData >= 13X There is a 0.44% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 93082560 0.37344966133504637 3.806672075111724 chr2 243199373 100143560 0.4117755681878341 20.786631531527505 chr3 198022430 68584971 0.3463495069725182 1.823036402264039 chr4 191154276 68521591 0.3584622454378159 3.406745737723607 chr5 180915260 64950894 0.35901279969417726 1.90083408347875 chr6 171115067 62044829 0.36259126731370767 3.257821119869445 chr7 159138663 58130900 0.3652845820377415 3.5137407100648606 chr8 146364022 50072312 0.34210806259478166 4.6563992004074874 chr9 141213431 47531523 0.33659350008994543 3.8172573174176487 chr10 135534747 50002875 0.36893030095079604 4.728222889125379 chr11 135006516 49190676 0.3643577914417109 2.317862474990516 chr12 133851895 45439402 0.3394752237164816 1.9596064527272343 chr13 115169878 35532757 0.30852474290195914 1.7277078185102615 chr14 107349540 30905513 0.2878960915901456 1.7633515551666956 chr15 102531392 32956026 0.3214237645383767 1.8515672769286675 chr16 90354753 33787221 0.3739396089102252 2.857524500330013 chr17 81195210 31093214 0.3829439445996876 2.7619018031248204 chr18 78077248 30005184 0.3843012499620888 5.033407666746025 chr19 59128983 22198924 0.3754321971003628 3.150282653684165 chr20 63025520 22652120 0.3594118699853647 2.0901924856594034 chr21 48129895 14413630 0.2994735392628636 2.4556628806018157 chr22 51304566 12782800 0.24915521164334575 1.7062925401845863 chrMT 16571 953438 57.53653973809668 46.09888275811287 chrX 155270560 26176460 0.16858611188109324 1.4134403997404434 chrY 59373566 9737395 0.16400219249084685 3.090088434019132