BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472682.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,589,830 number of mapped reads = 15,461,694 (99.18%) number of supplementary alignments = 91,480 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,750,812 number of mapped paired reads (second in pair) = 7,710,882 number of mapped paired reads (both in pair) = 15,382,714 number of mapped paired reads (singletons) = 78,980 number of mapped bases = 1,519,303,834 bp number of sequenced bases = 1,519,121,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,551,571 duplication rate = 47.73% >>>>>>> Insert size mean insert size = 19,812.9781 std insert size = 1,389,604.2884 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 55.0049 >>>>>>> ACTG content number of A's = 401,556,211 bp (26.43%) number of C's = 360,362,968 bp (23.72%) number of T's = 401,528,434 bp (26.43%) number of G's = 355,388,736 bp (23.39%) number of N's = 285,527 bp (0.02%) GC percentage = 47.12% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 8,904,426 number of insertions = 97,892 mapped reads with insertion percentage = 0.63% number of deletions = 78,437 mapped reads with deletion percentage = 0.5% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.4908X std coverageData = 22.5499X There is a 3.26% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% 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 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149485784 0.5997408688502325 23.133261066339234 chr2 243199373 147056657 0.6046753130403836 27.891289872772123 chr3 198022430 150512660 0.7600788456136004 26.898627697940476 chr4 191154276 58406507 0.30554643203482407 23.576158095756877 chr5 180915260 49371986 0.2729011693098747 15.078294818859977 chr6 171115067 98522161 0.5757655519604243 26.801548615874744 chr7 159138663 97449185 0.6123539255824966 26.79300431906163 chr8 146364022 77301805 0.5281475867067933 18.65110365558446 chr9 141213431 92691729 0.6563945677376821 21.83067742942767 chr10 135534747 34131347 0.2518272823425863 13.9066348568216 chr11 135006516 38126587 0.28240553218927594 14.890631518680244 chr12 133851895 58805107 0.43932965610983693 17.941577589960445 chr13 115169878 33060982 0.28706275090436406 10.235044705678922 chr14 107349540 27082414 0.25228253423349556 13.373381723719785 chr15 102531392 13496832 0.1316360944363264 6.510925278721884 chr16 90354753 88894931 0.9838434398686254 38.59357237773526 chr17 81195210 48137106 0.5928564751541378 17.887353946093064 chr18 78077248 23118701 0.2961003569183176 36.671504720817055 chr19 59128983 47533018 0.8038869533744559 20.573113351125915 chr20 63025520 67040163 1.0636986890389797 32.43867955189735 chr21 48129895 6377620 0.13250849601895037 6.8546572794463 chr22 51304566 13874226 0.27042867880414384 8.841157977837083 chrMT 16571 7132 0.43039044113209823 0.849636731353885 chrX 155270560 96283525 0.620101614884367 26.105199033493683 chrY 59373566 2535669 0.04270703565286949 5.12119044438019