BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504592.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 = 362,045,086 number of mapped reads = 346,108,211 (95.6%) number of supplementary alignments = 995,438 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 173,279,460 number of mapped paired reads (second in pair) = 172,828,751 number of mapped paired reads (both in pair) = 343,353,492 number of mapped paired reads (singletons) = 2,754,719 number of mapped bases = 33,254,486,822 bp number of sequenced bases = 33,243,839,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,709,556 duplication rate = 17.91% >>>>>>> Insert size mean insert size = 33,965.2396 std insert size = 1,750,282.1017 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.373 >>>>>>> ACTG content number of A's = 9,445,827,700 bp (28.41%) number of C's = 7,129,467,402 bp (21.45%) number of T's = 9,351,880,971 bp (28.13%) number of G's = 7,307,480,760 bp (21.98%) number of N's = 9,182,971 bp (0.03%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 191,044,541 number of insertions = 3,355,311 mapped reads with insertion percentage = 0.93% number of deletions = 4,123,492 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.4% >>>>>>> Coverage mean coverageData = 10.7422X std coverageData = 94.5143X There is a 90.86% of reference with a coverageData >= 1X There is a 89.08% of reference with a coverageData >= 2X There is a 86.05% of reference with a coverageData >= 3X There is a 81.83% of reference with a coverageData >= 4X There is a 76.57% of reference with a coverageData >= 5X There is a 70.56% of reference with a coverageData >= 6X There is a 64.1% of reference with a coverageData >= 7X There is a 57.5% of reference with a coverageData >= 8X There is a 51.01% of reference with a coverageData >= 9X There is a 44.8% of reference with a coverageData >= 10X There is a 39.02% of reference with a coverageData >= 11X There is a 33.75% of reference with a coverageData >= 12X There is a 29.03% of reference with a coverageData >= 13X There is a 24.86% of reference with a coverageData >= 14X There is a 21.23% of reference with a coverageData >= 15X There is a 18.1% of reference with a coverageData >= 16X There is a 15.42% of reference with a coverageData >= 17X There is a 13.15% of reference with a coverageData >= 18X There is a 11.22% of reference with a coverageData >= 19X There is a 9.61% of reference with a coverageData >= 20X There is a 8.25% of reference with a coverageData >= 21X There is a 7.12% of reference with a coverageData >= 22X There is a 6.18% of reference with a coverageData >= 23X There is a 5.39% of reference with a coverageData >= 24X There is a 4.72% of reference with a coverageData >= 25X There is a 4.17% of reference with a coverageData >= 26X There is a 3.7% of reference with a coverageData >= 27X There is a 3.31% of reference with a coverageData >= 28X There is a 2.98% of reference with a coverageData >= 29X There is a 2.7% of reference with a coverageData >= 30X There is a 2.46% of reference with a coverageData >= 31X There is a 2.25% of reference with a coverageData >= 32X There is a 2.07% of reference with a coverageData >= 33X There is a 1.92% of reference with a coverageData >= 34X There is a 1.78% of reference with a coverageData >= 35X There is a 1.66% of reference with a coverageData >= 36X There is a 1.56% of reference with a coverageData >= 37X There is a 1.46% of reference with a coverageData >= 38X There is a 1.38% of reference with a coverageData >= 39X There is a 1.3% of reference with a coverageData >= 40X There is a 1.23% of reference with a coverageData >= 41X There is a 1.17% of reference with a coverageData >= 42X There is a 1.11% of reference with a coverageData >= 43X There is a 1.06% of reference with a coverageData >= 44X There is a 1.01% of reference with a coverageData >= 45X There is a 0.97% of reference with a coverageData >= 46X There is a 0.93% of reference with a coverageData >= 47X There is a 0.89% of reference with a coverageData >= 48X There is a 0.85% of reference with a coverageData >= 49X There is a 0.82% of reference with a coverageData >= 50X There is a 0.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3091570943 12.403463351852592 171.3390695449231 chr2 243199373 2349661752 9.661463033459382 56.999142933980515 chr3 198022430 1966632258 9.931361098841176 16.248534588923988 chr4 191154276 1885613337 9.86435342414208 113.21033599960258 chr5 180915260 1570374551 8.680166344176826 10.236000754603188 chr6 171115067 1558017902 9.105088928259018 22.451495685689856 chr7 159138663 2804925758 17.62567125501111 135.6684606594945 chr8 146364022 2925256669 19.986173029598763 66.38610953511797 chr9 141213431 1199016882 8.490813327805908 60.27056964637812 chr10 135534747 1619256675 11.94717008620675 256.6989266579115 chr11 135006516 1427703387 10.575070221055109 38.38148232580919 chr12 133851895 1243042224 9.286698735195344 9.082995145679012 chr13 115169878 807192520 7.008712121758087 6.37041989121506 chr14 107349540 1078715208 10.048624409568966 9.382829150553524 chr15 102531392 869587446 8.481182485067597 7.207158589355061 chr16 90354753 923682038 10.222838393460053 72.97751833659072 chr17 81195210 1031011678 12.697937205901678 44.523154118405586 chr18 78077248 566939272 7.261260950181031 93.48569245397486 chr19 59128983 664819668 11.243549851009615 88.82594187102399 chr20 63025520 1397761017 22.17769908126105 28.73865878764585 chr21 48129895 398575670 8.281249522775813 40.01968697613127 chr22 51304566 448591089 8.74368743320039 9.387965670017532 chrMT 16571 118858489 7172.680526220505 1521.5085601051537 chrX 155270560 1180294513 7.601534463455274 18.553274505786792 chrY 59373566 127385876 2.145498149799525 114.85490161899632