BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156426.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 = 13,445,518 number of mapped reads = 13,144,679 (97.76%) number of supplementary alignments = 1,867,973 (13.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,572,415 number of mapped paired reads (second in pair) = 6,572,264 number of mapped paired reads (both in pair) = 12,953,870 number of mapped paired reads (singletons) = 190,809 number of mapped bases = 1,495,119,185 bp number of sequenced bases = 1,494,107,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,866,305 duplication rate = 65.87% >>>>>>> Insert size mean insert size = 1,059,419.4784 std insert size = 9,579,912.9561 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.3651 >>>>>>> ACTG content number of A's = 447,104,500 bp (29.92%) number of C's = 295,709,206 bp (19.79%) number of T's = 443,426,941 bp (29.68%) number of G's = 307,855,160 bp (20.6%) number of N's = 11,896 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 12,951,499 number of insertions = 166,674 mapped reads with insertion percentage = 1.22% number of deletions = 419,355 mapped reads with deletion percentage = 3.11% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.483X std coverageData = 8.9226X There is a 9.5% of reference with a coverageData >= 1X There is a 7.31% of reference with a coverageData >= 2X There is a 5.62% of reference with a coverageData >= 3X There is a 4.59% of reference with a coverageData >= 4X There is a 3.54% of reference with a coverageData >= 5X There is a 2.94% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 1.95% of reference with a coverageData >= 8X There is a 1.5% of reference with a coverageData >= 9X There is a 1.33% of reference with a coverageData >= 10X There is a 1.03% of reference with a coverageData >= 11X There is a 0.94% of reference with a coverageData >= 12X There is a 0.72% of reference with a coverageData >= 13X There is a 0.66% of reference with a coverageData >= 14X There is a 0.5% of reference with a coverageData >= 15X There is a 0.46% of reference with a coverageData >= 16X There is a 0.35% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% 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 0.01% 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 120639063 0.48400707093925355 3.8442888329790215 chr2 243199373 134889926 0.5546475072532362 29.832992204729923 chr3 198022430 100415843 0.5070932772615708 2.2206041638039236 chr4 191154276 100835120 0.52750648382043 3.6493823269143832 chr5 180915260 92914183 0.5135784731481469 2.2453014628858954 chr6 171115067 89334462 0.5220724484770239 2.981860883953083 chr7 159138663 82551864 0.5187417214885109 3.8413380007590407 chr8 146364022 74039547 0.5058589261779101 4.751118167128175 chr9 141213431 64369733 0.455832937024241 3.9602212066978395 chr10 135534747 74362195 0.5486577917912077 4.669093591617288 chr11 135006516 69424996 0.5142344092488099 2.420613484467476 chr12 133851895 67950318 0.5076530145501489 2.403570126886335 chr13 115169878 49390882 0.42885242962573944 2.0464797858084607 chr14 107349540 47247185 0.4401247084989838 2.164090191988153 chr15 102531392 44764565 0.4365937507217302 2.1901454344189024 chr16 90354753 45389023 0.5023423947603509 3.2059694293721797 chr17 81195210 41587556 0.5121922340000106 2.7016569319018617 chr18 78077248 41772753 0.5350182552540786 5.252131041499034 chr19 59128983 28669714 0.4848673619162366 3.035684056514086 chr20 63025520 32511679 0.5158494368630357 2.4621762319816667 chr21 48129895 20957279 0.4354316376547258 3.1096965835099573 chr22 51304566 19000289 0.3703430412022197 2.565191544920728 chrMT 16571 1532889 92.50431476676121 72.38454166046792 chrX 155270560 39550095 0.254717281885246 1.6161053695624163 chrY 59373566 11018026 0.1855712355225556 2.755680383013735