BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960918.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 = 230,533,412 number of mapped reads = 225,638,750 (97.88%) number of supplementary alignments = 465,635 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 113,352,705 number of mapped paired reads (second in pair) = 112,286,045 number of mapped paired reads (both in pair) = 223,586,492 number of mapped paired reads (singletons) = 2,052,258 number of mapped bases = 22,026,429,970 bp number of sequenced bases = 22,020,032,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,528,179 duplication rate = 12.3% >>>>>>> Insert size mean insert size = 18,977.3196 std insert size = 1,278,539.8402 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5702 >>>>>>> ACTG content number of A's = 6,750,173,722 bp (30.65%) number of C's = 4,269,609,852 bp (19.39%) number of T's = 6,746,439,736 bp (30.64%) number of G's = 4,250,847,081 bp (19.3%) number of N's = 2,962,030 bp (0.01%) GC percentage = 38.69% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 313,846,396 number of insertions = 2,634,953 mapped reads with insertion percentage = 1.14% number of deletions = 2,950,017 mapped reads with deletion percentage = 1.27% homopolymer indels = 40.43% >>>>>>> Coverage mean coverageData = 7.1152X std coverageData = 105.6654X There is a 89.49% of reference with a coverageData >= 1X There is a 85.35% of reference with a coverageData >= 2X There is a 79.27% of reference with a coverageData >= 3X There is a 71.71% of reference with a coverageData >= 4X There is a 63.25% of reference with a coverageData >= 5X There is a 54.49% of reference with a coverageData >= 6X There is a 45.94% of reference with a coverageData >= 7X There is a 38% of reference with a coverageData >= 8X There is a 30.89% of reference with a coverageData >= 9X There is a 24.73% of reference with a coverageData >= 10X There is a 19.55% of reference with a coverageData >= 11X There is a 15.28% of reference with a coverageData >= 12X There is a 11.84% of reference with a coverageData >= 13X There is a 9.12% of reference with a coverageData >= 14X There is a 6.99% of reference with a coverageData >= 15X There is a 5.34% of reference with a coverageData >= 16X There is a 4.08% of reference with a coverageData >= 17X There is a 3.12% of reference with a coverageData >= 18X There is a 2.4% of reference with a coverageData >= 19X There is a 1.85% of reference with a coverageData >= 20X There is a 1.44% of reference with a coverageData >= 21X There is a 1.13% of reference with a coverageData >= 22X There is a 0.91% of reference with a coverageData >= 23X There is a 0.74% of reference with a coverageData >= 24X There is a 0.61% of reference with a coverageData >= 25X There is a 0.52% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1829412160 7.339649356380139 279.68995040421663 chr2 243199373 1855103239 7.627911273439015 56.175912084937316 chr3 198022430 1640086856 8.282328703874606 9.618013408859337 chr4 191154276 1457060597 7.622432662714801 57.23704118077667 chr5 180915260 1197839673 6.620998543738102 9.491754366116862 chr6 171115067 1160147634 6.779926831340925 27.618723069186597 chr7 159138663 1211700183 7.614115640772978 69.15142046341894 chr8 146364022 1293599284 8.838232690817966 137.40154220736972 chr9 141213431 939398275 6.652329515313596 99.38122654369296 chr10 135534747 1048743616 7.73782103271274 202.52937031474502 chr11 135006516 1073725340 7.95313716561651 44.25370996403021 chr12 133851895 996145805 7.442149436883206 11.78676110782378 chr13 115169878 761957652 6.615945638146807 4.9388563265798044 chr14 107349540 468304970 4.362431082611066 7.431112398062915 chr15 102531392 591546272 5.769416180363571 5.232449747263236 chr16 90354753 721638897 7.986728678235665 86.90362686378907 chr17 81195210 417411664 5.140840992960053 26.1565047152183 chr18 78077248 846211147 10.838127222414396 102.1878502493266 chr19 59128983 404202498 6.835945377244185 117.61414445138857 chr20 63025520 412153865 6.53947583455083 18.865197805084712 chr21 48129895 293569132 6.099517399736691 22.831104066176575 chr22 51304566 225295336 4.39133109516997 5.806544694119875 chrMT 16571 4937759 297.9759217910808 59.82413752519185 chrX 155270560 1115995900 7.187427545827103 29.769430916616713 chrY 59373566 60242216 1.0146302480804337 53.26869074918779