BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504628.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 = 291,349,294 number of mapped reads = 271,858,886 (93.31%) number of supplementary alignments = 2,662,512 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 137,408,303 number of mapped paired reads (second in pair) = 134,450,583 number of mapped paired reads (both in pair) = 265,120,868 number of mapped paired reads (singletons) = 6,738,018 number of mapped bases = 25,936,291,075 bp number of sequenced bases = 25,912,154,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,541,253 duplication rate = 15.52% >>>>>>> Insert size mean insert size = 112,439.9898 std insert size = 3,132,219.1368 median insert size = 366 >>>>>>> Mapping quality mean mapping quality = 52.038 >>>>>>> ACTG content number of A's = 6,930,189,828 bp (26.74%) number of C's = 5,970,667,507 bp (23.04%) number of T's = 7,002,426,313 bp (27.02%) number of G's = 6,004,833,629 bp (23.17%) number of N's = 4,037,569 bp (0.02%) GC percentage = 46.22% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 355,044,268 number of insertions = 7,559,801 mapped reads with insertion percentage = 2.57% number of deletions = 7,290,264 mapped reads with deletion percentage = 2.5% homopolymer indels = 33.65% >>>>>>> Coverage mean coverageData = 8.3782X std coverageData = 193.2372X There is a 81.83% of reference with a coverageData >= 1X There is a 72.29% of reference with a coverageData >= 2X There is a 63.41% of reference with a coverageData >= 3X There is a 55.7% of reference with a coverageData >= 4X There is a 49% of reference with a coverageData >= 5X There is a 43.19% of reference with a coverageData >= 6X There is a 38.14% of reference with a coverageData >= 7X There is a 33.73% of reference with a coverageData >= 8X There is a 29.88% of reference with a coverageData >= 9X There is a 26.49% of reference with a coverageData >= 10X There is a 23.51% of reference with a coverageData >= 11X There is a 20.88% of reference with a coverageData >= 12X There is a 18.55% of reference with a coverageData >= 13X There is a 16.5% of reference with a coverageData >= 14X There is a 14.69% of reference with a coverageData >= 15X There is a 13.08% of reference with a coverageData >= 16X There is a 11.66% of reference with a coverageData >= 17X There is a 10.41% of reference with a coverageData >= 18X There is a 9.3% of reference with a coverageData >= 19X There is a 8.32% of reference with a coverageData >= 20X There is a 7.45% of reference with a coverageData >= 21X There is a 6.67% of reference with a coverageData >= 22X There is a 5.99% of reference with a coverageData >= 23X There is a 5.38% of reference with a coverageData >= 24X There is a 4.85% of reference with a coverageData >= 25X There is a 4.37% of reference with a coverageData >= 26X There is a 3.95% of reference with a coverageData >= 27X There is a 3.57% of reference with a coverageData >= 28X There is a 3.23% of reference with a coverageData >= 29X There is a 2.94% of reference with a coverageData >= 30X There is a 2.67% of reference with a coverageData >= 31X There is a 2.44% of reference with a coverageData >= 32X There is a 2.23% of reference with a coverageData >= 33X There is a 2.04% of reference with a coverageData >= 34X There is a 1.87% of reference with a coverageData >= 35X There is a 1.72% of reference with a coverageData >= 36X There is a 1.59% of reference with a coverageData >= 37X There is a 1.47% of reference with a coverageData >= 38X There is a 1.36% of reference with a coverageData >= 39X There is a 1.26% of reference with a coverageData >= 40X There is a 1.18% of reference with a coverageData >= 41X There is a 1.1% of reference with a coverageData >= 42X There is a 1.03% of reference with a coverageData >= 43X There is a 0.97% of reference with a coverageData >= 44X There is a 0.91% of reference with a coverageData >= 45X There is a 0.86% of reference with a coverageData >= 46X There is a 0.81% of reference with a coverageData >= 47X There is a 0.77% of reference with a coverageData >= 48X There is a 0.73% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.66% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1827320305 7.33125677949665 57.077889527132434 chr2 243199373 1975736985 8.123939468380126 223.9376257157283 chr3 198022430 1313863827 6.6349242709525384 21.84090486763964 chr4 191154276 1862429531 9.743070204717785 494.1362726972295 chr5 180915260 1585533887 8.763958811434701 31.82782062733356 chr6 171115067 759693225 4.439662960830913 24.326526175547205 chr7 159138663 1216496135 7.6442525786458315 32.39783210387969 chr8 146364022 1428042536 9.756786650752192 128.48499152464285 chr9 141213431 677344913 4.7966040354900805 71.24348636931934 chr10 135534747 1933595762 14.26642100862888 449.18076095330696 chr11 135006516 1051858232 7.791166405627414 23.783132704113978 chr12 133851895 977044530 7.299444882719068 18.894280734785898 chr13 115169878 393944677 3.420553045996975 10.723967729164583 chr14 107349540 665396489 6.198410249359243 28.218271116034895 chr15 102531392 888910250 8.669639928423091 16.10716290873189 chr16 90354753 1390687939 15.391419851482523 191.11810822542242 chr17 81195210 849151063 10.458142333765748 68.29307935694325 chr18 78077248 437637867 5.605190733669302 262.6153928473483 chr19 59128983 1027810725 17.382519922590248 38.78692284769263 chr20 63025520 767494898 12.177525833979633 121.60497324177047 chr21 48129895 496395793 10.313668729175495 160.30029087445746 chr22 51304566 464479498 9.053375444205102 28.569932808991943 chrMT 16571 8997418 542.9616800434494 246.1407371966427 chrX 155270560 1478499162 9.522083014320293 20.281814602397056 chrY 59373566 457925428 7.712614532871413 471.1452686903062