BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354862.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 = 21,196,724 number of mapped reads = 20,981,743 (98.99%) number of supplementary alignments = 378,913 (1.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,511,825 number of mapped paired reads (second in pair) = 10,469,918 number of mapped paired reads (both in pair) = 20,899,202 number of mapped paired reads (singletons) = 82,541 number of mapped bases = 2,908,286,005 bp number of sequenced bases = 2,906,599,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,914,059 duplication rate = 28.08% >>>>>>> Insert size mean insert size = 139,579.3473 std insert size = 4,129,057.7856 median insert size = 267 >>>>>>> Mapping quality mean mapping quality = 53.9243 >>>>>>> ACTG content number of A's = 832,475,329 bp (28.64%) number of C's = 612,695,341 bp (21.08%) number of T's = 838,305,340 bp (28.84%) number of G's = 623,073,909 bp (21.44%) number of N's = 49,111 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 24,306,131 number of insertions = 545,086 mapped reads with insertion percentage = 2.36% number of deletions = 521,001 mapped reads with deletion percentage = 2.31% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 0.9395X std coverageData = 18.832X There is a 40.74% of reference with a coverageData >= 1X There is a 22.83% of reference with a coverageData >= 2X There is a 10.69% of reference with a coverageData >= 3X There is a 5.94% of reference with a coverageData >= 4X There is a 2.83% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% 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 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 236158906 0.9474756975630564 26.399765916696808 chr2 243199373 254071290 1.0447037213373078 38.69151785429241 chr3 198022430 186028478 0.9394313462368884 1.7986887547727193 chr4 191154276 204425908 1.0694289046403544 26.179181223975316 chr5 180915260 169258814 0.935569581029262 1.6470796102816063 chr6 171115067 160847281 0.9399948456905902 3.3879916183521592 chr7 159138663 153023206 0.9615715195495893 11.603578877765763 chr8 146364022 145060302 0.9910926197423026 22.73291094083245 chr9 141213431 122406262 0.8668174205044278 12.866242980751348 chr10 135534747 164358520 1.2126670365939445 32.56570288176067 chr11 135006516 132009453 0.9778006048241404 3.821761117456574 chr12 133851895 125440851 0.9371615620384007 1.6236055927319977 chr13 115169878 87556906 0.7602413714460998 1.3712085840431776 chr14 107349540 85655213 0.797909455410801 2.4269968970644817 chr15 102531392 80974903 0.7897571799278801 1.3963965188218195 chr16 90354753 90352347 0.9999733716277217 6.783964091302372 chr17 81195210 79055030 0.97364154855933 5.357528309693574 chr18 78077248 81041747 1.0379687946993215 16.870847449474763 chr19 59128983 56441103 0.9545420897903825 14.612360448886468 chr20 63025520 61571802 0.9769344544876425 8.595896724190677 chr21 48129895 41805224 0.8685916310434503 13.356907326953543 chr22 51304566 36467736 0.7108087806453718 2.604234663570221 chrMT 16571 29237989 1764.407036388872 551.621598068767 chrX 155270560 77144368 0.4968383446288852 1.5904053807314136 chrY 59373566 47892366 0.8066277508074889 27.976905149377057