BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 15,331,876 number of mapped reads = 15,174,391 (98.97%) number of supplementary alignments = 483,374 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,594,676 number of mapped paired reads (second in pair) = 7,579,715 number of mapped paired reads (both in pair) = 15,146,762 number of mapped paired reads (singletons) = 27,629 number of mapped bases = 1,899,925,268 bp number of sequenced bases = 1,899,107,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,685,306 duplication rate = 75.02% >>>>>>> Insert size mean insert size = 314,928.0528 std insert size = 6,482,955.3133 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 53.8529 >>>>>>> ACTG content number of A's = 545,867,980 bp (28.74%) number of C's = 391,502,602 bp (20.62%) number of T's = 557,557,401 bp (29.36%) number of G's = 404,174,910 bp (21.28%) number of N's = 4,930 bp (0%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 12,193,273 number of insertions = 287,262 mapped reads with insertion percentage = 1.79% number of deletions = 313,160 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.6137X std coverageData = 23.4211X There is a 10.32% of reference with a coverageData >= 1X There is a 9.4% of reference with a coverageData >= 2X There is a 6.51% of reference with a coverageData >= 3X There is a 6.08% of reference with a coverageData >= 4X There is a 4.29% of reference with a coverageData >= 5X There is a 4% of reference with a coverageData >= 6X There is a 2.86% of reference with a coverageData >= 7X There is a 2.66% of reference with a coverageData >= 8X There is a 1.93% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.31% of reference with a coverageData >= 11X There is a 1.21% of reference with a coverageData >= 12X There is a 0.9% of reference with a coverageData >= 13X There is a 0.82% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.57% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.4% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% 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 0.01% 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 151587762 0.6081740594740584 18.77432377444681 chr2 243199373 179601653 0.7384955429140847 78.13198295905421 chr3 198022430 128320931 0.6480121014573955 2.7646121721145285 chr4 191154276 133310656 0.6973982418264083 6.496396373958705 chr5 180915260 117649156 0.6502997922894951 2.529185619942664 chr6 171115067 109456326 0.6396650389646868 3.5406633951086652 chr7 159138663 104132475 0.6543505709860086 11.882132714018677 chr8 146364022 95821278 0.6546778141967157 3.642324497438216 chr9 141213431 82206119 0.5821409367215219 9.436428463010527 chr10 135534747 100018247 0.7379528070392163 18.34734284672742 chr11 135006516 87591006 0.6487909516900651 4.438592811532548 chr12 133851895 83608845 0.6246369915046777 2.491291632122406 chr13 115169878 62326267 0.5411681255753349 2.2928398758335238 chr14 107349540 57936771 0.5397020890820771 4.421296958367347 chr15 102531392 52864603 0.515594316714241 2.2147649310670285 chr16 90354753 56156502 0.6215113221547958 4.432415167544949 chr17 81195210 48454476 0.5967652032675327 4.382478732152174 chr18 78077248 52686310 0.6747972213364898 8.243776092168645 chr19 59128983 32217520 0.5448684953705359 9.27188514231511 chr20 63025520 38023641 0.6033054705458994 3.0773687220014008 chr21 48129895 26506143 0.5507209812113656 3.9028979923223694 chr22 51304566 20396358 0.3975544398913734 2.2709213664545316 chrMT 16571 7453725 449.80538289783357 101.92495744555391 chrX 155270560 51864675 0.3340277448603264 2.207938943553515 chrY 59373566 19733823 0.3323671514020229 8.029653370154502