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Table 1 Nucleotide polymorphisms in C. intestinalis sp. A loci.

From: SNPs and Hox gene mapping in Ciona intestinalis

Gene bp nH Ts     Tv       Ts/Tv ∑SNPs(ts+tv) 1 bp indel ∑PS ∑SNPs/PS π fSNPs f∑PS T93 L'sP
    AG CT ∑Ts % AC AT GC GT ∑Tv %           
Hox1 573 4 1 3 4 40 2 3 1 0 6 60 0.67 10 4 16 0.62 0.017 0.020 0.03 0.007 0.012
Hox2 531 3 1 0 1 50 0 1 0 0 1 50 0.5 2 1 3 0.67 0.002 0.004 0.005 0.000002 0.000066
Hox4 357 3 0 0 0 0 0 1 0 0 1 100 0 1 1 2 1 0.002 0.006 0.006 0.0028 0.0062
Hox5 481 11 10 8 18 72 1 6 0 0 7 28 2.57 25 3 45 0.55 0.024 0.052 0.093 0.004 0.004
Hox10 531 8 10 5 15 43 1 15 0 4 20 57 0.75 35 8 61 0.57 0.038 0.066 0.115 0.004 0.003
EvxA 569 3 0 0 0 0 0 2 0 0 2 100 0 2 1 3 0.67 0.002 0.003 0.005 0.0035 0.0039
Xlox 707 5 3 2 5 55 0 1 3 0 4 45 1.25 9 1 16 0.56 0.006 0.013 0.022 0.000002 0.0018
Gsx 186 6 1 1 2 100 0 0 0 0 0 0 0 2 0 15 0.13 0.012 0.01 0.08 0.0035 0.003706
Wd-40 1340 4 2 0 2 28 3 1 0 1 5 72 0.4 7 3 30 0.23 0.008 0.005 0.028 0.0084 0.231
ci0100134706 678 4 6 6 12 70 0 2 0 3 5 30 2.4 17 7 38 0.45 0.019 0.025 0.056 0.03 0.04
  5953   34 25 59 54 7 32 4 8 51 46 1.18 110 29 229 0.48   0.019 0.038   
Gsx 897 4 5 8 13 87 0 2 0 0 2 13 6.5 15 0 15 1 0.011 0.017 0.017 0.00452 0.004575
Hox13 601 2 1 1 2 67 0 0 0 1 1 33 2 3 3 11 0.27 0.008 0.005 0.025 0.01188 0.016926
COI 515 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
  2013   6 9 15 83 0 2 0 1 3 17 5.0 18 3 26 0.69   0.009 0.013   
  1. Abbreviations: bp, length of the amplified sequence; nH, number of haplotypes; Ts, transition; Tv, transversion; ∑, total; PS, polymorphic sites; π, nucleotide diversity; f, frequency; T93, Tamura-Nei genetic distance (1993); L'sP, Lake's paralinear genetic distance.
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BMC Genomics

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