BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504620.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 = 551,416,168 number of mapped reads = 501,420,645 (90.93%) number of supplementary alignments = 5,071,549 (0.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 253,622,318 number of mapped paired reads (second in pair) = 247,798,327 number of mapped paired reads (both in pair) = 486,829,576 number of mapped paired reads (singletons) = 14,591,069 number of mapped bases = 47,860,369,969 bp number of sequenced bases = 47,819,142,281 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,133,070 duplication rate = 27.12% >>>>>>> Insert size mean insert size = 105,080.3136 std insert size = 3,042,278.0552 median insert size = 327 >>>>>>> Mapping quality mean mapping quality = 52.0552 >>>>>>> ACTG content number of A's = 12,869,016,939 bp (26.91%) number of C's = 10,969,728,458 bp (22.94%) number of T's = 12,961,711,997 bp (27.11%) number of G's = 10,968,020,856 bp (22.94%) number of N's = 50,664,031 bp (0.11%) GC percentage = 45.88% >>>>>>> Mismatches and indels general error rate = 0.0189 number of mismatches = 846,970,173 number of insertions = 14,064,283 mapped reads with insertion percentage = 2.6% number of deletions = 12,550,138 mapped reads with deletion percentage = 2.33% homopolymer indels = 34.09% >>>>>>> Coverage mean coverageData = 15.4603X std coverageData = 364.0166X There is a 87.41% of reference with a coverageData >= 1X There is a 82.5% of reference with a coverageData >= 2X There is a 77.24% of reference with a coverageData >= 3X There is a 72.13% of reference with a coverageData >= 4X There is a 67.24% of reference with a coverageData >= 5X There is a 62.67% of reference with a coverageData >= 6X There is a 58.42% of reference with a coverageData >= 7X There is a 54.49% of reference with a coverageData >= 8X There is a 50.84% of reference with a coverageData >= 9X There is a 47.45% of reference with a coverageData >= 10X There is a 44.31% of reference with a coverageData >= 11X There is a 41.4% of reference with a coverageData >= 12X There is a 38.68% of reference with a coverageData >= 13X There is a 36.14% of reference with a coverageData >= 14X There is a 33.78% of reference with a coverageData >= 15X There is a 31.56% of reference with a coverageData >= 16X There is a 29.49% of reference with a coverageData >= 17X There is a 27.56% of reference with a coverageData >= 18X There is a 25.75% of reference with a coverageData >= 19X There is a 24.05% of reference with a coverageData >= 20X There is a 22.46% of reference with a coverageData >= 21X There is a 20.98% of reference with a coverageData >= 22X There is a 19.58% of reference with a coverageData >= 23X There is a 18.28% of reference with a coverageData >= 24X There is a 17.07% of reference with a coverageData >= 25X There is a 15.93% of reference with a coverageData >= 26X There is a 14.87% of reference with a coverageData >= 27X There is a 13.88% of reference with a coverageData >= 28X There is a 12.95% of reference with a coverageData >= 29X There is a 12.09% of reference with a coverageData >= 30X There is a 11.29% of reference with a coverageData >= 31X There is a 10.54% of reference with a coverageData >= 32X There is a 9.84% of reference with a coverageData >= 33X There is a 9.19% of reference with a coverageData >= 34X There is a 8.58% of reference with a coverageData >= 35X There is a 8.02% of reference with a coverageData >= 36X There is a 7.49% of reference with a coverageData >= 37X There is a 7% of reference with a coverageData >= 38X There is a 6.55% of reference with a coverageData >= 39X There is a 6.13% of reference with a coverageData >= 40X There is a 5.73% of reference with a coverageData >= 41X There is a 5.37% of reference with a coverageData >= 42X There is a 5.03% of reference with a coverageData >= 43X There is a 4.72% of reference with a coverageData >= 44X There is a 4.42% of reference with a coverageData >= 45X There is a 4.15% of reference with a coverageData >= 46X There is a 3.9% of reference with a coverageData >= 47X There is a 3.66% of reference with a coverageData >= 48X There is a 3.44% of reference with a coverageData >= 49X There is a 3.24% of reference with a coverageData >= 50X There is a 3.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3688829426 14.799679981539544 111.7475297112094 chr2 243199373 3777261084 15.53154121001784 363.8639035187522 chr3 198022430 2567911977 12.967783381912847 32.95951534558314 chr4 191154276 3613246443 18.902252769904035 1010.8521646402976 chr5 180915260 2498467434 13.81015307387558 48.29275710503307 chr6 171115067 2058609905 12.030558974681055 46.012643519960065 chr7 159138663 2355963038 14.804466705868956 53.08983038063021 chr8 146364022 2251742923 15.384538442104304 270.9038456294122 chr9 141213431 1745699174 12.362132706767815 125.96013730820872 chr10 135534747 3157030556 23.293145306863632 810.176646819389 chr11 135006516 2052874435 15.205743365749843 43.81045201432209 chr12 133851895 1916909685 14.321124740146562 27.4322136898455 chr13 115169878 1072874534 9.315582795008257 20.480310262379156 chr14 107349540 1278090331 11.905876177951018 44.25759867861707 chr15 102531392 1392799818 13.584130585099244 22.980349289010306 chr16 90354753 2140318975 23.68795114740671 292.40894490129045 chr17 81195210 1626074989 20.026735431806877 104.91670961196697 chr18 78077248 1083304560 13.874778988111876 409.79942791982785 chr19 59128983 1579547818 26.713596917437258 61.23273210515954 chr20 63025520 1218809674 19.33835173434507 254.17554757823532 chr21 48129895 795395731 16.526022568717426 345.68818676026586 chr22 51304566 873896412 17.033501696515668 44.26629349670183 chrMT 16571 18139342 1094.6437752700501 503.024514887894 chrX 155270560 2356258088 15.175176079741066 31.209819621842005 chrY 59373566 740313617 12.468741005045915 855.074559395008