BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617424.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 22,889,296 number of mapped reads = 18,624,634 (81.37%) number of supplementary alignments = 262,239 (1.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,113,370 number of mapped paired reads (second in pair) = 8,511,264 number of mapped paired reads (both in pair) = 16,819,904 number of mapped paired reads (singletons) = 1,804,730 number of mapped bases = 1,803,330,226 bp number of sequenced bases = 1,802,946,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 565,762 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 59,743.7186 std insert size = 2,348,572.2155 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.3032 >>>>>>> ACTG content number of A's = 539,630,090 bp (29.93%) number of C's = 359,632,257 bp (19.95%) number of T's = 534,874,173 bp (29.67%) number of G's = 368,611,875 bp (20.44%) number of N's = 197,889 bp (0.01%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0182 number of mismatches = 32,507,005 number of insertions = 151,085 mapped reads with insertion percentage = 0.8% number of deletions = 174,229 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.5825X std coverageData = 1.845X There is a 23.23% of reference with a coverageData >= 1X There is a 11.64% of reference with a coverageData >= 2X There is a 6.66% of reference with a coverageData >= 3X There is a 4.21% of reference with a coverageData >= 4X There is a 2.84% of reference with a coverageData >= 5X There is a 2% of reference with a coverageData >= 6X There is a 1.46% of reference with a coverageData >= 7X There is a 1.1% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% 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 0.02% 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 115674004 0.4640871245813265 1.723668565243976 chr2 243199373 180034134 0.7402738410842861 1.9824566154798586 chr3 198022430 152606811 0.7706541678132118 2.1435237730667307 chr4 191154276 87809714 0.45936568010647066 1.474556488538927 chr5 180915260 116032811 0.6413655266006859 1.8367269442390337 chr6 171115067 83577177 0.4884267555468976 1.6643009970026046 chr7 159138663 134978455 0.8481814064254141 2.060741329451354 chr8 146364022 80182496 0.5478292746013771 2.029781070423316 chr9 141213431 72149814 0.5109274202111838 1.6427617921680253 chr10 135534747 57686157 0.4256189521643479 1.5155452418911615 chr11 135006516 133233901 0.9868701522525032 2.4044286527710645 chr12 133851895 85937597 0.642034967080593 1.7768014308242825 chr13 115169878 78693272 0.6832799805518592 1.7842185691038883 chr14 107349540 52160755 0.4858963997423743 1.8003077966304828 chr15 102531392 41212800 0.401952994064491 1.5065255699805844 chr16 90354753 44859935 0.49648672051596443 2.052077678382174 chr17 81195210 54608226 0.6725547726275971 2.2517869596276743 chr18 78077248 25953066 0.3324024176671801 1.272124836396361 chr19 59128983 25090392 0.4243332241990362 1.440884958783588 chr20 63025520 60533532 0.9604606514948231 2.89219900119184 chr21 48129895 24714650 0.5134989386534087 1.606929698366178 chr22 51304566 14278104 0.2783008436325141 1.2857178115881482 chrMT 16571 108347 6.538350129744734 3.867197078722059 chrX 155270560 79716172 0.5134017163330898 1.6378276453758094 chrY 59373566 1497904 0.02522846614939719 0.3854501553890286