Table 2.
Genomic frequencies of the SNPs in the CENP-C haplotypes in Region01 and Region02.
| SNP | Name | Change | Polymorphism type | Position | Coverage | Variant coverage | Genomic detected | Transcriptome proportion | Missing haplotype for more common SNP | Missing haplotype for variant SNP | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genomic variant | Genomic | Genomic proportion | P-value (binomial test) | Genomic variant | Genomic | Genomic proportion | P-value (binomial test) | |||||||||
| 1 | G | C -> G | SNP (transversion) | 106 | 16 | 13 | Yes | 0.81 | 5 | 3 | 0.63 | 1.95E-01* | 4 | 4 | 0.5 | 2.13E-02 |
| 2 | G | A -> G | SNP (transition) | 150 | 19 | 8 | Yes | 0.42 | 1 | 7 | 0.13 | 1.25E-03 | 2 | 6 | 0.25 | 1.08E-01* |
| 3 | C | G -> C | SNP (transversion) | 246 | 34 | 7 | Yes | 0.21 | 1 | 7 | 0.13 | 1.87E-01* | 2 | 6 | 0.25 | 6.93E-01* |
| 4 | T | A -> T | SNP (transversion) | 369 | 65 | 7 | Yes | 0.11 | 1 | 7 | 0.13 | 8.51E-01* | 2 | 6 | 0.25 | 6.14E-03 |
| 5 | A | G -> A | SNP (transition) | 371 | 68 | 19 | No | 0.28 | 1 | 7 | 0.13 | 6.21E-04 | 1 | 7 | 0.13 | 6.21E-04 |
| 6 | C | T -> C | SNP (transition) | 390 | 64 | 15 | No | 0.23 | 1 | 7 | 0.13 | 1.32E-02 | 1 | 7 | 0.13 | 1.32E-02 |
| 7 | G | T -> G | SNP (transversion) | 513 | 46 | 12 | Yes | 0.26 | 3 | 5 | 0.38 | 1.28E-01* | 4 | 4 | 0.5 | 1.64E-03 |
| 8 | A | G -> A | SNP (transition) | 518 | 45 | 10 | Yes | 0.22 | 2 | 6 | 0.25 | 7.34E-01* | 3 | 5 | 0,375 | 4.40E-02 |
| 9 | T | G -> T | SNP (transversion) | 731 | 54 | 8 | Yes | 0.15 | 2 | 6 | 0.25 | 1.14E-01* | 3 | 5 | 0,375 | 3.58E-04 |
| 10 | C | A -> C | SNP (transversion) | 1008 | 56 | 9 | No | 0.16 | 1 | 7 | 0.13 | 4.17E-01* | 1 | 7 | 0.13 | 4.17E-01* |
| 11 | T | C -> T | SNP (transition) | 1061 | 91 | 29 | Yes | 0.32 | 2 | 6 | 0.25 | 1.46E-01* | 3 | 5 | 0,375 | 2.81E-01* |
| 12 | T | C -> T | SNP (transition) | 1088 | 77 | 41 | Yes | 0.53 | 4 | 4 | 0.50 | 6.48E-01* | 3 | 5 | 0,375 | 6.37E-03 |
| 13 | T | C -> T | SNP (transition) | 1190 | 76 | 9 | Yes | 0.12 | 2 | 6 | 0.25 | 7.49E-03 | 3 | 5 | 0,375 | 1.10E-06 |
| 14 | A | G -> A | SNP (transition) | 1209 | 76 | 20 | No | 0.26 | 1 | 7 | 0.13 | 1.31E-03 | 1 | 7 | 0.13 | 1.31E-03 |
| 15 | T | A -> T | SNP (transversion) | 1251 | 62 | 10 | Yes | 0.16 | 2 | 6 | 0.25 | 1.41E-01* | 3 | 5 | 0,375 | 3.29E-04 |
| 16 | G | A -> G | SNP (transition) | 1255 | 62 | 55 | Yes | 0.89 | 6 | 2 | 0.75 | 1.19E-02 | 5 | 3 | 0,625 | 5.15E-06 |
| 17 | -ATG | Deletion | 1307 | 75 | 9 | Yes | 0.12 | 1 | 7 | 0.13 | 1.00E+00* | 2 | 6 | 0.25 | 7.38E-03 | |
| 18 | G | A -> G | SNP (transition) | 1314 | 90 | 23 | Yes | 0.26 | 1 | 7 | 0.13 | 6.50E-04 | 2 | 6 | 0.25 | 9.03E-01* |
| 19 | G | T -> G | SNP (transversion) | 1347 | 103 | 13 | Yes | 0.13 | 2 | 6 | 0.25 | 2.88E-03 | 3 | 5 | 0,375 | 3.09E-08 |
| 20 | A | T -> A | SNP (transversion) | 1384 | 101 | 37 | Yes | 0.37 | 1 | 7 | 0.13 | 5.30E-10 | 2 | 6 | 0.25 | 1.09E-02 |
| 21 | G | C -> G | SNP (transversion) | 1424 | 80 | 9 | No | 0.11 | 1 | 7 | 0.13 | 8.66E-01* | 1 | 7 | 0.13 | 8.66E-01* |
| 22 | A | C -> A | SNP (transversion) | 1437 | 84 | 10 | Yes | 0.12 | 1 | 7 | 0.13 | 1.00E+00* | 2 | 6 | 0.25 | 5.12E-03 |
| 23 | TT | AA -> TT | Substitution | 1481 | 62 | 7 | No | 0.11 | 1 | 7 | 0.13 | 1.00E+00* | 1 | 7 | 0.13 | 1.00E+00* |
| 24 | G | A -> G | SNP (transition) | 1527 | 106 | 90 | Yes (duplication) | 0.85 | ||||||||
| 25 | C | T -> C | SNP (transition) | 1540 | 139 | 86 | Yes (duplication) | 0.62 | ||||||||
| 26 | A | T -> A | SNP (transversion) | 1584 | 253 | 235 | Yes (duplication) | 0.93 | ||||||||
| 27 | A | G -> A | SNP (transition) | 1638 | 247 | 39 | Yes (duplication) | 0.16 | ||||||||
| 28 | C | A -> C | SNP (transversion) | 1648 | 209 | 106 | Yes (duplication) | 0.51 | ||||||||
| 29 | A | C -> A | SNP (transversion) | 1739 | 122 | 16 | Yes (duplication) | 0.13 | ||||||||
| 30 | T | C -> T | SNP (transition) | 1751 | 132 | 32 | Yes (duplication) | 0.24 | ||||||||
| 31 | A | G -> A | SNP (transition) | 1753 | 138 | 16 | Yes (duplication) | 0.12 | ||||||||
| 32 | A | C -> A | SNP (transversion) | 1762 | 131 | 21 | No (duplication) | 0.16 | ||||||||
| 33 | T | A -> T | SNP (transversion) | 1776 | 125 | 75 | Yes (duplication) | 0.6 | ||||||||
| 34 | C | G -> C | SNP (transversion) | 1796 | 88 | 31 | No (duplication) | 0.35 | ||||||||
| 35 | G | C -> G | SNP (transversion) | 1808 | 37 | 25 | Yes | 0.68 | 4 | 3 | 0.57 | 0.00E+00* | 4 | 4 | 0.57 | 8.90E-01* |
| 36 | T | C -> T | SNP (transition) | 1808 | 78 | 41 | Yes (duplication) | 0.53 | ||||||||
| 37 | T | C -> T | SNP (transition) | 1814 | 78 | 27 | Yes (duplication) | 0.35 | ||||||||
| 38 | T | C -> T | SNP (transition) | 1827 | 68 | 7 | Yes (duplication) | 0.1 | ||||||||
| 39 | A | T -> A | SNP (transversion) | 1830 | 65 | 8 | Yes (duplication) | 0.12 | ||||||||
| 40 | A | G -> A | SNP (transition) | 1839 | 62 | 23 | Yes (duplication) | 0.37 | ||||||||
| 41 | A | G -> A | SNP (transition) | 1853 | 52 | 6 | Yes (duplication) | 0.12 | ||||||||
| 42 | C | A -> C | SNP (transversion) | 1866 | 47 | 30 | Yes (duplication) | 0.64 | ||||||||
| 43 | A | C -> A | SNP (transversion) | 1910 | 152 | 34 | Yes (duplication) | 0.22 | ||||||||
| 44 | A | G -> A | SNP (transition) | 1917 | 158 | 103 | Yes (duplication) | 0.65 | ||||||||
| 45 | G | T -> G | SNP (transversion) | 1922 | 165 | 110 | Yes (duplication) | 0.67 | ||||||||
| 46 | T | A -> T | SNP (transversion) | 1938 | 170 | 41 | Yes (duplication) | 0.24 | ||||||||
| 47 | A | C -> A | SNP (transversion) | 2039 | 196 | 37 | Yes (duplication) | 0.19 | ||||||||
| 48 | T | C -> T | SNP (transition) | 2043 | 196 | 143 | Yes (duplication) | 0.73 | ||||||||
| 49 | G | T -> G | SNP (transversion) | 2080 | 177 | 88 | Yes (duplication) | 0.5 | ||||||||
| 50 | C | A -> C | SNP (transversion) | 2123 | 126 | 89 | Yes (duplication) | 0.71 | ||||||||
Genome and transcriptome SNPs were used. The global expression (in diverse tissues) was used to determine whether the genomic frequency could explain the transcription frequency (H0). The binomial test was used to verify H0. The
“*”
in p-values reflect the acceptance of H0.