Table 2. SNP Characteristics and Primers.
SNP locations (based upon O157 Sakai chromosome), amino acid change, and SNP type are listed. The corresponding bases as determined by sequencing are listed for each strain and are color-coded to denote the ancestral (blue) or variant (orange for radial SNPs, green for linear SNPs) designation. An ‘X’ at strain 87-07’s site 2392896 indicates our inability to amplify by PCR at this site. Primers used for PCR amplification of the each SNP are reported.
| Location | Amino Acid Change | SNP Type | 86-17 | 86-24 | 86-28 | 87-07 | 87-23 | U-39 | EK15 | EK28 | O157 Sakai | Forward Primer | Reverse Primer |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3798 | Synonymous | Radial | G | T | T | G | T | G | G | G | G | AATGAGCAGGTCAGCTTTGC | GACATCGCTTTCAACATTGG |
| 505838 | Synonymous | Radial | T | T | T | T | T | A | A | A | A | TTCTTCGGTACGTTTGAGCA | TCATCAACCTCCATCAGTGC |
| 795801 | Synonymous | Radial | T | T | T | T | T | C | C | C | C | ATGGTCAACATTCCCTGCAC | GGAGTCTGCGTGTGCAAATA |
| 1098382 | Synonymous | Radial | T | T | T | T | T | C | C | C | C | TTGTCGTGGTTGGTAATCTCACC | TGACGATTACCGCATCAACTGAC |
| 1894260 | Synonymous | Radial | A | A | A | A | A | T | T | T | T | CGCCTGTTCAAGCTGGTATT | GGCGTAAAGATATCCGGTCA |
| 1977261 | Synonymous | Radial | T | T | T | T | T | G | G | G | G | CCATCACTACCAAGGCCATAA | TGAAGAAGTGGTTGATGAATTGC |
| 2388580 | Synonymous | Radial | C | T | T | C | T | C | C | C | C | ATGGTGAAGATAAGCGACTGTTGG | TTGCCGCTGGTCTGATAGATG |
| 2436199 | Synonymous | Radial | A | A | A | A | A | G | G | G | G | GGCGCACAACTGACATTTATC | GGTTAAAGGTCAGCGACAGG |
| 2984974 | Synonymous | Radial | C | A | A | C | A | C | C | C | C | AAAATGGCTCCTTGTTGTGG | TGGTTGAAGCCTTTCGTAGG |
| 4258114 | Synonymous | Radial | G | G | G | G | G | A | A | A | A | CCCTGAAATTTGACCTGCTG | CCATGGAACAACCGTTACAG |
| 4259164 | Synonymous | Radial | G | G | G | G | G | A | A | A | A | GGTTTTACCGTTGGTTTTGC | AATCAGCGTAGCCATTACCG |
| 5153038 | Synonymous | Radial | C | T | T | C | T | C | C | C | C | ATGACGCCTGAACATACCAGC | TACTATACGGAAGCCACAGTCGG |
| 5234150 | Synonymous | Radial | A | A | A | A | A | C | C | C | C | TCAATGCTGAACCACACAGC | GTTTGGCCTGAACCCAGAGT |
| 5391618 | Synonymous | Radial | C | A | A | C | A | C | C | C | C | AAAATGGCTCCTTGTTGTGG | TGGTTGAAGCCTTTCGTAGG |
| 30477 | Nonsynonymous | Radial | T | T | T | T | T | C | C | C | C | ACGCTAAAACTCGACGATGG | ATGCTGATAGCGCGGTCTAC |
| 79307 | Nonsynonymous | Radial | T | A | A | T | A | T | T | T | T | ATATCGCGGGTACGACAGAG | AAAAGGTGAAAGCGATCTGG |
| 571478 | Nonsynonymous | Radial | A | G | G | A | G | A | A | A | A | TGATTCAGGAGCTGCAACAG | CACCGGAATCAGCTGGTAGT |
| 1330848 | Nonsynonymous | Radial | A | A | A | A | A | G | G | G | G | CCGCCAACAATCCACATAAT | CATCCCTCAGGCTAAAGACAA |
| 1480429 | Nonsynonymous | Radial | C | C | C | C | C | T | T | T | T | ATTCGAGGTTCAATGCGTTT | GCGAATTGAAGTCACCATAGC |
| 1492372 | Nonsynonymous | Radial | A | G | G | A | G | A | A | A | A | ATGCAGATCAACCTGAATTCCAGC | AGCAGTTGGGTTTGTTCGTTG |
| 2392896 | Nonsynonymous | Radial | A | A | A | X | A | T | T | T | A | GCAATGTGTGGTTGAGATCG | TGCATCGTGCCTATCTTTCA |
| 2422218 | Nonsynonymous | Radial | A | A | A | A | A | T | T | T | A | CGCAGATTAATGCTGAAGAGG | TTAGTGAAGAATCCGGTAATGG |
| 3006720 | Nonsynonymous | Radial | A | A | A | A | A | C | C | C | A | ATACACAAGCTTTGCGAGTAAC | AAGAGTTGTGTGGCTTCTTGC |
| 3714794 | Nonsynonymous | Radial | A | A | A | A | A | G | G | G | A | TTCAACGCGTTAGAGAACAATC | AATGCAGCGCAAAGAATAGA |
| 4007883 | Nonsynonymous | Radial | T | C | C | T | C | T | T | T | T | TCCTTCTGTCATGATCCGAATCC | ATACCTGGTGCTAGTGCTTCG |
| 4378660 | Nonsynonymous | Radial | T | T | T | T | T | C | C | C | C | TCGCTGATGCTGTAGAGGTG | TCTTTCTGAACTGGGCAACC |
| 4678681 | Nonsynonymous | Radial | G | A | A | G | A | G | G | G | G | GATTATACAGGTTGGCGATAAGC | GACATCAAGCGCATACTCGAC |
| 4912166 | Nonsynonymous | Radial | A | A | A | A | A | G | G | G | A | ATCGAAAGTAGGGGCTCCAG | CAGTGAGAAAAGCACCAGCA |
| 5094375 | Nonsynonymous | Radial | G | G | G | G | G | A | A | A | G | ATTCGAGGTTCAATGCGTTT | GCGAATTGAAGTCACCATAGC |
| 5103324 | Nonsynonymous | Radial | A | A | A | A | A | G | G | G | G | GAACCAGGCGTGATGAGTG | AACTTTCCGTGTCGTTGAGC |
| 5155031 | Nonsynonymous | Radial | A | A | A | A | A | G | G | G | G | TAGCGATTCAGCGTCGAGTA | AACGCTGTGGTGTATCGTTG |
| 5286625 | Nonsynonymous | Radial | G | C | C | G | C | G | G | G | G | TGGTGATGTTGTATGTGAATCC | TGATGACCTGATGGATCACATC |
| 358636 | Nonsynonymous | Linear | G | G | A | G | ACTCACCTTCATAGCGGAAAG | AGACGGAGTGTAGATTAGTCAAC | |||||
| 2030050 | Nonsynonymous | Linear | A | A | G | A | ATTACGACATCATTCTCCGCA | AAGGTTTGTCGTGGACGTG | |||||
| 2373421 | Nonsynonymous | Linear | A | A | A | A | ATATGATGATGGGTGGACTGG | ACTGTGGCGGATAGGATAAGC | |||||
| 4660184 | Nonsynonymous | Linear | G | G | G | G | TCTCTGACTTTGGATGAACGG | TCACTCACATTCATCACGATGG | |||||
| 4757979 | Nonsynonymous | Linear | T | T | T | T | AACCTGAACGACGACGATTAC | ATCGTGTCGGTTTGTTGACAG | |||||
| 421747 | Synonymous | Linear | T | T | C | T | ATAATATCGGTTGCGGAGGTG | ATCCTCTGCATGGTCAGGTC | |||||
| 2100062 | Synonymous | Linear | A | A | A | A | TGTAGAGACTCAGCATTGCTTAG | TACAGATAACCCTGACCAACG | |||||
| 3008913 | Synonymous | Linear | A | A | A | A | TACAGATTTCCTGGTCATCGG | TCTACTCTCCCTGTTGTCTGG | |||||
| 4143190 | Synonymous | Linear | T | T | T | T | GATGACCGTGCAGTTTATCG | GTATGCGGCAGGCCTATAAC | |||||
| 4962486 | Synonymous | Linear | T | T | C | T | TTCTCGAAACCATTACCTGCC | TCTTCACTATCCAGCAGTACG | |||||
| 5303294 | Synonymous | Linear | C | C | C | T | AAGCAATTTAGCGCTCGACAC | TTGGTCATCCAGTGACTGTTG |