BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618666.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 462,571,116 number of mapped reads = 420,200,474 (90.84%) number of supplementary alignments = 1,341,366 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 211,682,859 number of mapped paired reads (second in pair) = 208,517,615 number of mapped paired reads (both in pair) = 410,651,478 number of mapped paired reads (singletons) = 9,548,996 number of mapped bases = 41,304,892,592 bp number of sequenced bases = 41,292,561,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,377,058 duplication rate = 25.29% >>>>>>> Insert size mean insert size = 42,079.9601 std insert size = 1,950,333.215 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.6185 >>>>>>> ACTG content number of A's = 12,446,520,561 bp (30.14%) number of C's = 8,215,682,071 bp (19.9%) number of T's = 12,339,365,392 bp (29.88%) number of G's = 8,275,013,656 bp (20.04%) number of N's = 15,979,722 bp (0.04%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 446,183,351 number of insertions = 4,166,801 mapped reads with insertion percentage = 0.96% number of deletions = 4,969,922 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 13.3427X std coverageData = 145.1437X There is a 92.16% of reference with a coverageData >= 1X There is a 91.73% of reference with a coverageData >= 2X There is a 90.91% of reference with a coverageData >= 3X There is a 89.55% of reference with a coverageData >= 4X There is a 87.52% of reference with a coverageData >= 5X There is a 84.75% of reference with a coverageData >= 6X There is a 81.19% of reference with a coverageData >= 7X There is a 76.9% of reference with a coverageData >= 8X There is a 71.95% of reference with a coverageData >= 9X There is a 66.48% of reference with a coverageData >= 10X There is a 60.64% of reference with a coverageData >= 11X There is a 54.61% of reference with a coverageData >= 12X There is a 48.58% of reference with a coverageData >= 13X There is a 42.7% of reference with a coverageData >= 14X There is a 37.09% of reference with a coverageData >= 15X There is a 31.87% of reference with a coverageData >= 16X There is a 27.11% of reference with a coverageData >= 17X There is a 22.83% of reference with a coverageData >= 18X There is a 19.06% of reference with a coverageData >= 19X There is a 15.79% of reference with a coverageData >= 20X There is a 12.98% of reference with a coverageData >= 21X There is a 10.6% of reference with a coverageData >= 22X There is a 8.62% of reference with a coverageData >= 23X There is a 6.97% of reference with a coverageData >= 24X There is a 5.62% of reference with a coverageData >= 25X There is a 4.52% of reference with a coverageData >= 26X There is a 3.64% of reference with a coverageData >= 27X There is a 2.93% of reference with a coverageData >= 28X There is a 2.36% of reference with a coverageData >= 29X There is a 1.91% of reference with a coverageData >= 30X There is a 1.56% of reference with a coverageData >= 31X There is a 1.28% of reference with a coverageData >= 32X There is a 1.06% of reference with a coverageData >= 33X There is a 0.89% of reference with a coverageData >= 34X There is a 0.75% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.44% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.36% of reference with a coverageData >= 41X There is a 0.34% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3352613398 13.45077249777444 323.215486966727 chr2 243199373 3586905413 14.748826729088648 91.314632622872 chr3 198022430 2801796476 14.148884426880329 17.78619693912774 chr4 191154276 2887744523 15.10687902686519 81.56492824681067 chr5 180915260 2557414668 14.135980944890996 12.531069886555116 chr6 171115067 2440994742 14.26522389171025 60.43238632961907 chr7 159138663 2252933438 14.157046411782408 100.07462286191677 chr8 146364022 2140182840 14.622328703156299 191.77617702783357 chr9 141213431 1769036271 12.527393877994509 150.7288452427317 chr10 135534747 2177625888 16.06691963648259 350.6121020867618 chr11 135006516 1893165687 14.02277270083764 71.92781574110344 chr12 133851895 1844864147 13.782876566670947 11.347287691387182 chr13 115169878 1380432873 11.986058307711327 8.974960704021202 chr14 107349540 1261117106 11.747764415199171 13.49629096287102 chr15 102531392 1161521974 11.328452207105508 9.29538529784671 chr16 90354753 1249401240 13.8277312318036 111.81543776877474 chr17 81195210 1065138898 13.11824796068635 60.55762348146161 chr18 78077248 1180147536 15.115127213500148 178.67968005833333 chr19 59128983 739997760 12.514975270249447 141.80333569984052 chr20 63025520 831356649 13.190793967269132 45.25015973287781 chr21 48129895 583559564 12.124679765040003 67.07151902812008 chr22 51304566 469314816 9.147622767143181 63.709097009655544 chrMT 16571 19246691 1161.4682879729648 204.81031256131095 chrX 155270560 1142153081 7.35588949379715 31.266568411117074 chrY 59373566 516226913 8.6945579957249 169.84824859283495