BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174035.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 = 1,575,230 number of mapped reads = 1,532,271 (97.27%) number of supplementary alignments = 155,251 (9.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 766,685 number of mapped paired reads (second in pair) = 765,586 number of mapped paired reads (both in pair) = 1,505,516 number of mapped paired reads (singletons) = 26,755 number of mapped bases = 181,763,067 bp number of sequenced bases = 181,656,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,167,982 duplication rate = 62.97% >>>>>>> Insert size mean insert size = 1,177,237.2246 std insert size = 10,206,355.7949 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.9816 >>>>>>> ACTG content number of A's = 54,711,324 bp (30.12%) number of C's = 35,595,091 bp (19.59%) number of T's = 54,480,215 bp (29.99%) number of G's = 36,867,820 bp (20.3%) number of N's = 2,313 bp (0%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 1,959,245 number of insertions = 20,027 mapped reads with insertion percentage = 1.25% number of deletions = 43,836 mapped reads with deletion percentage = 2.79% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 1.0017X There is a 1.31% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14384811 0.05771223735486701 0.8174586818399768 chr2 243199373 16117792 0.06627398665209552 2.500663850534047 chr3 198022430 12498266 0.06311540566389373 0.7074563879909624 chr4 191154276 12791875 0.06691911511307233 0.8414672621734526 chr5 180915260 11305527 0.062490731848711935 0.7046194691530113 chr6 171115067 10852018 0.06341941823276147 0.754352900728972 chr7 159138663 9608028 0.06037519618975308 0.7795436895736446 chr8 146364022 9292754 0.06349069855432095 0.86059006804744 chr9 141213431 8080057 0.057218757045850686 0.7617095800525128 chr10 135534747 8929328 0.06588220509977416 0.8939335739701073 chr11 135006516 8517271 0.063087851256009 0.7110456277050773 chr12 133851895 8392715 0.06270150303064442 0.7012696602506 chr13 115169878 5916765 0.05137424040685361 0.6463368820050162 chr14 107349540 5583358 0.05201101001457482 0.6428875181007979 chr15 102531392 5264362 0.051343904508777176 0.632790141649711 chr16 90354753 5707115 0.0631634176455554 0.7920447930897692 chr17 81195210 4986490 0.061413598166689884 0.7370207357004657 chr18 78077248 5159409 0.06608082549220998 0.9479503723451104 chr19 59128983 3240401 0.05480224478070255 0.7310785385897326 chr20 63025520 3904084 0.06194449486493725 0.700560858070714 chr21 48129895 2630965 0.054663842503707934 0.7273303568428191 chr22 51304566 2234331 0.04355033429188349 0.5779443592169223 chrMT 16571 210752 12.718122020397079 11.903178654773004 chrX 155270560 4849849 0.03123482648610271 0.48653814503761134 chrY 59373566 1304744 0.021975166524442882 0.5222333219256308