BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960896.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 = 220,574,048 number of mapped reads = 216,936,532 (98.35%) number of supplementary alignments = 386,691 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 108,688,833 number of mapped paired reads (second in pair) = 108,247,699 number of mapped paired reads (both in pair) = 215,787,550 number of mapped paired reads (singletons) = 1,148,982 number of mapped bases = 21,340,796,174 bp number of sequenced bases = 21,334,539,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,016,325 duplication rate = 9.59% >>>>>>> Insert size mean insert size = 15,327.2078 std insert size = 1,160,599.8081 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.6388 >>>>>>> ACTG content number of A's = 6,522,657,771 bp (30.57%) number of C's = 4,151,499,762 bp (19.46%) number of T's = 6,512,879,993 bp (30.53%) number of G's = 4,146,432,200 bp (19.44%) number of N's = 1,069,494 bp (0.01%) GC percentage = 38.89% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 249,615,334 number of insertions = 2,542,394 mapped reads with insertion percentage = 1.14% number of deletions = 2,693,868 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 6.8937X std coverageData = 93.7841X There is a 89.28% of reference with a coverageData >= 1X There is a 84.95% of reference with a coverageData >= 2X There is a 78.6% of reference with a coverageData >= 3X There is a 70.81% of reference with a coverageData >= 4X There is a 62.19% of reference with a coverageData >= 5X There is a 53.38% of reference with a coverageData >= 6X There is a 44.88% of reference with a coverageData >= 7X There is a 37.03% of reference with a coverageData >= 8X There is a 30.03% 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 14.63% of reference with a coverageData >= 12X There is a 11.21% of reference with a coverageData >= 13X There is a 8.5% of reference with a coverageData >= 14X There is a 6.38% of reference with a coverageData >= 15X There is a 4.76% of reference with a coverageData >= 16X There is a 3.52% of reference with a coverageData >= 17X There is a 2.6% of reference with a coverageData >= 18X There is a 1.92% of reference with a coverageData >= 19X There is a 1.42% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 0.8% of reference with a coverageData >= 22X There is a 0.61% of reference with a coverageData >= 23X There is a 0.48% 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 0.2% 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 1807670681 7.25242197490854 232.68658972028203 chr2 243199373 2243580863 9.225274042955695 50.236465188912014 chr3 198022430 1403923181 7.089717972857923 13.905114239251835 chr4 191154276 1189771478 6.224142629171424 76.76496764444737 chr5 180915260 1153883847 6.378034926406982 8.176777682332954 chr6 171115067 1307326337 7.6400422237511085 27.286096773646772 chr7 159138663 1105346714 6.945808725312717 58.89047380438692 chr8 146364022 1219518313 8.332090744267742 95.84458563568846 chr9 141213431 1080710642 7.653030128557672 76.35952952680886 chr10 135534747 949283871 7.003988954950423 220.95014534206126 chr11 135006516 945828485 7.005798779371508 36.42306270523406 chr12 133851895 1077539139 8.050234469971457 7.804096943048303 chr13 115169878 599999775 5.209693588457218 4.678140623802307 chr14 107349540 423751800 3.9474021034463678 6.810430916672456 chr15 102531392 521192608 5.083249118474857 4.575642782518087 chr16 90354753 578176779 6.3989636383600095 85.11157932867586 chr17 81195210 454703956 5.600132766452602 24.149836232699922 chr18 78077248 673701387 8.628651806477606 80.50012316220203 chr19 59128983 370715425 6.269605973097829 102.79186432471532 chr20 63025520 412484260 6.544718076106314 22.406207560846536 chr21 48129895 267011908 5.547735103099643 30.89158615228928 chr22 51304566 244971600 4.774849864240154 6.16878296343447 chrMT 16571 8422732 508.28145555488504 110.92844657823659 chrX 155270560 1241598283 7.996353481303861 25.48907511230629 chrY 59373566 59682110 1.0051966560337642 65.83567436278722