JME-2004-00087 Supplementary Material

Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences

Wei Zhang†, Gerard G. Bouffard‡, Susan S. Wallace§, NISC Comparative Sequencing Program‡ and Jeffrey P. Bond§*

†Department of Human Genetics, University of Chicago, 920 E. 58th St., 515 CLSC, Chicago, IL 60637, USA

‡ Genome Technology Branch, National Human Genome Research Institute, and

NIH Intramural Sequencing Center, National Institutes of Health, Bethesda, MD 20892, USA* To whom correspondence should be addressed

§Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405-0068, USA

Tel: (802) 656-4608

Fax: (802) 656-8749

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Keywords: mutation, transition mutation, transversion mutation, maximum likelihood, genomics, molecular evolution, substitution, CpG dinucleotide

Supplementary Material: Relative nearest neighbor sequence context-dependent mutation rates

Mutation / Class* / No. of Mutations / Triplet Frequency / ML Rate
T-1 / T-2 / T-1 / T-2 / T-1 / T-2
AAA(TTT)->ACA(TGT) / 4 / 170 / 8 / 79905.5 / 6355.5 / 1.34E-03 / 7.68E-04
AAA(TTT)->AGA(TCT) / 2 / 240 / 17 / 79905.5 / 6355.5 / 1.98E-03 / 1.33E-03
AAA(TTT)->ATA(TAT) / 4 / 77 / 8 / 79905.5 / 6355.5 / 6.36E-04 / 6.07E-04
AAC(GTT)->ACC(GGT) / 4 / 30 / 6 / 27413 / 3353.5 / 6.89E-04 / 7.97E-04
AAC(GTT)->AGC(GCT) / 2 / 142 / 14 / 27413 / 3353.5 / 3.62E-03 / 3.12E-03
AAC(GTT)->ATC(GAT) / 4 / 24 / 3 / 27413 / 3353.5 / 4.95E-04 / 4.70E-04
AAG(CTT)->ACG(CGT) / 4 / 47 / 9 / 39367.5 / 5791 / 8.10E-04 / 6.41E-04
AAG(CTT)->AGG(CCT) / 2 / 160 / 22 / 39367.5 / 5791 / 2.59E-03 / 2.42E-03
AAG(CTT)->ATG(CAT) / 4 / 36 / 5 / 39367.5 / 5791 / 6.21E-04 / 3.98E-04
AAT(ATT)->ACT(AGT) / 4 / 59 / 3 / 51740.5 / 3718.5 / 8.16E-04 / 3.45E-04
AAT(ATT)->AGT(ACT) / 2 / 362 / 16 / 51740.5 / 3718.5 / 4.35E-03 / 2.70E-03
AAT(ATT)->ATT(AAT) / 4 / 56 / 6 / 51740.5 / 3718.5 / 7.33E-04 / 6.22E-04
ACA(TGT)->AAA(TTT) / 4 / 91 / 5 / 36325.5 / 4936.5 / 1.60E-03 / 5.12E-04
ACA(TGT)->AGA(TCT) / 4 / 59 / 6 / 36325.5 / 4936.5 / 1.10E-03 / 1.04E-03
ACA(TGT)->ATA(TAT) / 2 / 361 / 40 / 36325.5 / 4936.5 / 6.79E-03 / 4.56E-03
ACC(GGT)->AAC(GTT) / 4 / 75 / 13 / 18922 / 4499.5 / 2.22E-03 / 1.24E-03
ACC(GGT)->AGC(GCT) / 4 / 41 / 6 / 18922 / 4499.5 / 1.34E-03 / 6.57E-04
ACC(GGT)->ATC(GAT) / 2 / 172 / 30 / 18922 / 4499.5 / 6.03E-03 / 3.87E-03
ACG(CGT)->AAG(CTT) / 3 / 9 / 6 / 1440 / 1238 / 3.44E-03 / 1.72E-03
ACG(CGT)->AGG(CCT) / 3 / 8 / 6 / 1440 / 1238 / 3.29E-03 / 1.84E-03
ACG(CGT)->ATG(CAT) / 1 / 175 / 70 / 1440 / 1238 / 8.13E-02 / 2.54E-02
ACT(AGT)->AAT(ATT) / 4 / 62 / 7 / 30631 / 3754 / 1.40E-03 / 8.04E-04
ACT(AGT)->AGT(ACT) / 4 / 69 / 11 / 30631 / 3754 / 1.61E-03 / 1.29E-03
ACT(AGT)->ATT(AAT) / 2 / 241 / 26 / 30631 / 3754 / 4.94E-03 / 3.95E-03
CAA(TTG)->CCA(TGG) / 4 / 64 / 7 / 35793.5 / 4411 / 1.28E-03 / 9.59E-04
CAA(TTG)->CGA(TCG) / 2 / 206 / 25 / 35793.5 / 4411 / 2.63E-03 / 2.90E-03
CAA(TTG)->CTA(TAG) / 4 / 31 / 2 / 35793.5 / 4411 / 5.15E-04 / 1.62E-04
CAC(GTG)->CCC(GGG) / 4 / 35 / 10 / 24238.5 / 5383.5 / 1.11E-03 / 1.14E-03
CAC(GTG)->CGC(GCG) / 2 / 191 / 40 / 24238.5 / 5383.5 / 3.50E-03 / 4.18E-03
CAC(GTG)->CTC(GAG) / 4 / 31 / 3 / 24238.5 / 5383.5 / 7.17E-04 / 5.77E-04
CAG(CTG)->CCG(CGG) / 4 / 48 / 10 / 33480.5 / 9160.5 / 9.88E-04 / 1.01E-03
CAG(CTG)->CGG(CCG) / 2 / 244 / 60 / 33480.5 / 9160.5 / 3.18E-03 / 3.35E-03
CAG(CTG)->CTG(CAG) / 4 / 45 / 7 / 33480.5 / 9160.5 / 8.51E-04 / 5.51E-04
CAT(ATG)->CCT(AGG) / 4 / 63 / 9 / 34093.5 / 4011.5 / 1.24E-03 / 9.12E-04
CAT(ATG)->CGT(ACG) / 2 / 499 / 52 / 34093.5 / 4011.5 / 5.12E-03 / 5.75E-03
CAT(ATG)->CTT(AAG) / 4 / 55 / 6 / 34093.5 / 4011.5 / 1.18E-03 / 8.75E-04
CCA(TGG)->CAA(TTG) / 4 / 61 / 15 / 30914.5 / 7646.5 / 1.25E-03 / 8.23E-04
CCA(TGG)->CGA(TCG) / 4 / 40 / 7 / 30914.5 / 7646.5 / 7.47E-04 / 4.83E-04
CCA(TGG)->CTA(TAG) / 2 / 186 / 55 / 30914.5 / 7646.5 / 4.53E-03 / 3.88E-03
CCC(GGG)->CAC(GTG) / 4 / 44 / 14 / 18798.5 / 9163.5 / 1.46E-03 / 8.31E-04
CCC(GGG)->CGC(GCG) / 4 / 42 / 14 / 18798.5 / 9163.5 / 1.14E-03 / 8.65E-04
CCC(GGG)->CTC(GAG) / 2 / 163 / 67 / 18798.5 / 9163.5 / 5.80E-03 / 3.99E-03
CCG(CGG)->CAG(CTG) / 3 / 2 / 3 / 1395.5 / 2540.5 / 1.52E-03 / 1.03E-03
CCG(CGG)->CGG(CCG) / 3 / 8 / 9 / 1395.5 / 2540.5 / 3.51E-03 / 2.82E-03
CCG(CGG)->CTG(CAG) / 1 / 125 / 119 / 1395.5 / 2540.5 / 6.02E-02 / 2.25E-02
CCT(AGG)->CAT(ATG) / 4 / 49 / 14 / 30252 / 8216 / 8.93E-04 / 6.56E-04
CCT(AGG)->CGT(ACG) / 4 / 64 / 14 / 30252 / 8216 / 1.19E-03 / 8.21E-04
CCT(AGG)->CTT(AAG) / 2 / 245 / 54 / 30252 / 8216 / 5.19E-03 / 3.82E-03
GAA(TTC)->GCA(TGC) / 4 / 33 / 7 / 39397.5 / 5511.5 / 5.27E-04 / 6.36E-04
GAA(TTC)->GGA(TCC) / 2 / 122 / 32 / 39397.5 / 5511.5 / 2.16E-03 / 2.72E-03
GAA(TTC)->GTA(TAC) / 4 / 36 / 2 / 39397.5 / 5511.5 / 5.38E-04 / 1.56E-04
GAC(GTC)->GCC(GGC) / 4 / 12 / 7 / 15835 / 3838 / 4.55E-04 / 9.35E-04
GAC(GTC)->GGC(GCC) / 2 / 77 / 15 / 15835 / 3838 / 3.61E-03 / 2.54E-03
GAC(GTC)->GTC(GAC) / 4 / 17 / 2 / 15835 / 3838 / 5.18E-04 / 3.33E-04
GAG(CTC)->GCG(CGC) / 4 / 28 / 9 / 28404.5 / 6954.5 / 5.05E-04 / 7.75E-04
GAG(CTC)->GGG(CCC) / 2 / 93 / 28 / 28404.5 / 6954.5 / 2.28E-03 / 2.28E-03
GAG(CTC)->GTG(CAC) / 4 / 36 / 4 / 28404.5 / 6954.5 / 7.44E-04 / 4.43E-04
GAT(ATC)->GCT(AGC) / 4 / 29 / 2 / 25061.5 / 3277 / 7.97E-04 / 8.50E-04
GAT(ATC)->GGT(ACC) / 2 / 134 / 13 / 25061.5 / 3277 / 3.79E-03 / 2.43E-03
GAT(ATC)->GTT(AAC) / 4 / 38 / 7 / 25061.5 / 3277 / 8.50E-04 / 7.96E-04
GCA(TGC)->GAA(TTC) / 4 / 67 / 10 / 24432 / 5615.5 / 1.77E-03 / 8.45E-04
GCA(TGC)->GGA(TCC) / 4 / 33 / 7 / 24432 / 5615.5 / 9.83E-04 / 7.52E-04
GCA(TGC)->GTA(TAC) / 2 / 144 / 40 / 24432 / 5615.5 / 4.63E-03 / 3.12E-03
GCC(GGC)->GAC(GTC) / 4 / 61 / 17 / 17350.5 / 7539 / 1.85E-03 / 8.85E-04
GCC(GGC)->GGC(GCC) / 4 / 33 / 10 / 17350.5 / 7539 / 1.30E-03 / 8.43E-04
GCC(GGC)->GTC(GAC) / 2 / 135 / 37 / 17350.5 / 7539 / 5.83E-03 / 3.49E-03
GCG(CGC)->GAG(CTC) / 3 / 15 / 7 / 1443 / 2126 / 6.46E-03 / 1.93E-03
GCG(CGC)->GGG(CCC) / 3 / 5 / 7 / 1443 / 2126 / 1.72E-03 / 1.61E-03
GCG(CGC)->GTG(CAC) / 1 / 82 / 60 / 1443 / 2126 / 4.23E-02 / 1.55E-02
GCT(AGC)->GAT(ATC) / 4 / 38 / 4 / 23415 / 6140.5 / 9.81E-04 / 6.75E-04
GCT(AGC)->GGT(ACC) / 4 / 40 / 13 / 23415 / 6140.5 / 1.09E-03 / 9.75E-04
GCT(AGC)->GTT(AAC) / 2 / 166 / 40 / 23415 / 6140.5 / 5.05E-03 / 4.03E-03
TAA(TTA)->TCA(TGA) / 4 / 60 / 5 / 44072.5 / 3077.5 / 1.18E-03 / 1.08E-03
TAA(TTA)->TGA(TCA) / 2 / 197 / 12 / 44072.5 / 3077.5 / 2.86E-03 / 2.33E-03
TAA(TTA)->TTA(TAA) / 4 / 96 / 2 / 44072.5 / 3077.5 / 1.16E-03 / 3.87E-04
TAC(GTA)->TCC(GGA) / 4 / 17 / 5 / 21170.5 / 2196 / 7.59E-04 / 1.04E-03
TAC(GTA)->TGC(GCA) / 2 / 121 / 13 / 21170.5 / 2196 / 4.55E-03 / 2.98E-03
TAC(GTA)->TTC(GAA) / 4 / 17 / 4 / 21170.5 / 2196 / 6.03E-04 / 9.39E-04
TAG(CTA)->TCG(CGA) / 4 / 23 / 4 / 24892 / 2362 / 6.71E-04 / 8.73E-04
TAG(CTA)->TGG(CCA) / 2 / 138 / 11 / 24892 / 2362 / 4.11E-03 / 2.98E-03
TAG(CTA)->TTG(CAA) / 4 / 27 / 5 / 24892 / 2362 / 7.40E-04 / 1.00E-03
TAT(ATA)->TCT(AGA) / 4 / 61 / 5 / 39809.5 / 2227 / 1.03E-03 / 1.18E-03
TAT(ATA)->TGT(ACA) / 2 / 412 / 23 / 39809.5 / 2227 / 6.75E-03 / 6.66E-03
TAT(ATA)->TTT(AAA) / 4 / 66 / 2 / 39809.5 / 2227 / 1.16E-03 / 4.18E-04
TCA(TGA)->TAA(TTA) / 4 / 60 / 8 / 38058.5 / 5094.5 / 1.12E-03 / 6.91E-04
TCA(TGA)->TGA(TCA) / 4 / 66 / 10 / 38058.5 / 5094.5 / 1.07E-03 / 8.92E-04
TCA(TGA)->TTA(TAA) / 2 / 209 / 25 / 38058.5 / 5094.5 / 3.54E-03 / 2.89E-03
TCC(GGA)->TAC(GTA) / 4 / 42 / 10 / 26679.5 / 6995 / 1.21E-03 / 5.85E-04
TCC(GGA)->TGC(GCA) / 4 / 41 / 14 / 26679.5 / 6995 / 1.28E-03 / 1.30E-03
TCC(GGA)->TTC(GAA) / 2 / 178 / 42 / 26679.5 / 6995 / 4.83E-03 / 2.93E-03
TCG(CGA)->TAG(CTA) / 3 / 9 / 2 / 1456.5 / 1116.5 / 4.08E-03 / 6.02E-04
TCG(CGA)->TGG(CCA) / 3 / 4 / 7 / 1456.5 / 1116.5 / 2.55E-03 / 3.42E-03
TCG(CGA)->TTG(CAA) / 1 / 112 / 38 / 1456.5 / 1116.5 / 5.09E-02 / 1.72E-02
TCT(AGA)->TAT(ATA) / 4 / 100 / 7 / 42377.5 / 6211 / 1.52E-03 / 5.81E-04
TCT(AGA)->TGT(ACA) / 4 / 138 / 15 / 42377.5 / 6211 / 2.05E-03 / 1.92E-03
TCT(AGA)->TTT(AAA) / 2 / 241 / 46 / 42377.5 / 6211 / 3.66E-03 / 3.30E-03

*Class 1, CpG transitios; 2, other transitions; 3, CpG transversions; 4, other transversions

T1: Target-1

T2: Target-2

1