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Table 1 Validation of the CoSSA SNPs

From: Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

SNP R allele donor Association with P2 resistance* Association with P6 resistance* Association with P18 resistance* χ2 χ2 test significance
chr00_20792298 Kuba 2.1E−14 1.2E−14 8.3E−15 1.5 ns
chr00_20801212 Kuba 1.3E−14 7.3E−15 4.8E−15 1.2 ns
chr00_20858042 Kuba 2.1E−14 1.2E−14 8.3E−15 1.5 ns
chr00_20872536 Kuba 1.3E−14 7.3E−15 4.8E−15 1.2 ns
chr03_15683229 Ludmilla 6.8E−01 6.9E−01 3.0E−01 0.1 ns
chr04_64488861 Ludmilla 6.6E−01 9.7E−01 3.8E−01 0.1 ns
chr04_65204393 Ludmilla 4.5E−01 1.1E−01 2.0E−01 1.5 ns
chr05_2117034 Ludmilla 3.8E−01 9.4E−02 1.4E−01 0.0 ns
chr05_8795719 Ludmilla 2.0E−01 9.0E−02 1.6E−01 0.0 ns
chr05_9254557 Ludmilla 2.3E−01 8.4E−02 1.8E−01 0.0 ns
chr09_55113777 Ludmilla 2.4E−03 9.0E−04 4.2E−03 0.0 ns
chr09_55354021 Ludmilla 4.6E−03 1.3E−03 5.9E−03 0.1 ns
chr11_799292 Kuba 7.3E−13 6.7E−14 1.5E−13 0.4 ns
chr11_1259552 Kuba 2.0E−12 1.8E−13 4.5E−13 0.8 ns
chr11_1680269 Kuba 2.2E−14 1.2E−14 7.7E−15 1.5 ns
chr11_1772869 Kuba 2.9E−13 1.8E−13 1.4E−13 0.6 ns
chr11_1919971 Kuba 2.2E−13 1.4E−13 1.1E−13 0.8 ns
chr11_2040481 Kuba 2.2E−13 1.4E−13 1.1E−13 0.8 ns
chr11_2298154 Kuba 2.1E−12 9.7E−12 1.1E−12 1.8 ns
chr11_2687396 Kuba 3.6E−11 6.0E−11 1.9E−11 2.1 ns
chr11_2815640 Kuba 2.5E−11 5.5E−11 1.4E−11 1.5 ns
chr11_3325292 Kuba 1.2E−09 4.6E−09 7.7E−10 2.1 ns
chr11_4362386 Kuba 1.0E−09 3.0E−08 3.4E−09 1.0 ns
chr11_5505183 Kuba 4.8E−06 6.4E−04 4.3E−04 6.5 < 0.01
  1. χ2 tests: null hypothesis: the marker follows a 1:1 segregation pattern
  2. ns not significant
  3. *p-values of association between KASP marker results and Glynne-Lemmerzahl tests of 2016 (Kruskal–Wallis tests)