BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960898.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 220,838,488 number of mapped reads = 217,442,821 (98.46%) number of supplementary alignments = 380,611 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 108,962,232 number of mapped paired reads (second in pair) = 108,480,589 number of mapped paired reads (both in pair) = 216,229,764 number of mapped paired reads (singletons) = 1,213,057 number of mapped bases = 21,343,733,829 bp number of sequenced bases = 21,337,527,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,968,539 duplication rate = 9.56% >>>>>>> Insert size mean insert size = 15,351.5447 std insert size = 1,164,539.2889 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.6263 >>>>>>> ACTG content number of A's = 6,516,674,455 bp (30.54%) number of C's = 4,156,910,875 bp (19.48%) number of T's = 6,508,460,477 bp (30.5%) number of G's = 4,151,294,630 bp (19.46%) number of N's = 4,186,813 bp (0.02%) GC percentage = 38.94% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 271,198,620 number of insertions = 2,538,986 mapped reads with insertion percentage = 1.14% number of deletions = 2,698,332 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 6.8947X std coverageData = 93.5741X There is a 89.3% of reference with a coverageData >= 1X There is a 84.99% of reference with a coverageData >= 2X There is a 78.65% of reference with a coverageData >= 3X There is a 70.87% of reference with a coverageData >= 4X There is a 62.25% of reference with a coverageData >= 5X There is a 53.44% of reference with a coverageData >= 6X There is a 44.92% of reference with a coverageData >= 7X There is a 37.05% of reference with a coverageData >= 8X There is a 30.04% of reference with a coverageData >= 9X There is a 23.97% of reference with a coverageData >= 10X There is a 18.85% of reference with a coverageData >= 11X There is a 14.62% of reference with a coverageData >= 12X There is a 11.2% of reference with a coverageData >= 13X There is a 8.49% of reference with a coverageData >= 14X There is a 6.37% of reference with a coverageData >= 15X There is a 4.74% of reference with a coverageData >= 16X There is a 3.51% of reference with a coverageData >= 17X There is a 2.59% of reference with a coverageData >= 18X There is a 1.91% of reference with a coverageData >= 19X There is a 1.41% of reference with a coverageData >= 20X There is a 1.05% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.61% of reference with a coverageData >= 23X There is a 0.47% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1809748850 7.260759643202654 233.6207929103936 chr2 243199373 2243782314 9.226102379795197 49.79410301082324 chr3 198022430 1402857261 7.08433514829608 13.848481857137253 chr4 191154276 1189352576 6.221951195065079 75.12890513951575 chr5 180915260 1153627740 6.3766193078461155 8.140318574941666 chr6 171115067 1308443041 7.646568265084453 27.376300501421138 chr7 159138663 1107055714 6.956547787510317 59.071267542391574 chr8 146364022 1219246803 8.330235711888268 93.69145669069987 chr9 141213431 1081118842 7.655920788441151 75.92460434942804 chr10 135534747 948310357 6.996806191699314 219.75300145863554 chr11 135006516 944847591 6.99853324857298 36.00158892362058 chr12 133851895 1078880397 8.060254933260378 7.8110998182969675 chr13 115169878 600697628 5.215752924562445 4.67040900050524 chr14 107349540 424114453 3.9507803480108064 6.753735107774448 chr15 102531392 521260922 5.083915392468289 4.575032832711044 chr16 90354753 578658959 6.4043001589523465 85.25964398647946 chr17 81195210 454083186 5.5924873647103075 24.0840491077959 chr18 78077248 673060803 8.620447316483286 79.27444902767999 chr19 59128983 370829654 6.271537834499877 102.13990091228186 chr20 63025520 412809401 6.549876954605055 21.947597377729718 chr21 48129895 266833810 5.54403474181691 30.57721527963946 chr22 51304566 245275510 4.780773508541131 6.140680188755245 chrMT 16571 8396851 506.7196306801038 110.28119248256237 chrX 155270560 1241224197 7.99394422870633 25.432117377362438 chrY 59373566 59216969 0.9973625131426332 64.89984346220908