A chisq test for samples identified as having the germplasm_type listed below. Deviations from the expected allele ratios below are calculated. If dnasample_group or dnasample_group_cycle[3] fields are provided, the chisq tests are carried out by these fields. H0 (Null Hypothesis): Samples across marker support expected segregation ratio of specified germplasm population. H1 (Alternative Hypothesis): Reject H0
Calculation: Zygotes of samples grouped by meta field criteria, with missing values excluded, are counted as nz.The total number of zygotes are ntotal. The following formulation is performed on all zygotes to calculate Chisq using lookup tables in the Germplasm Population Distributions section below: Field | Description |
---|
germplasm_type |
| dnasample_sample_group |
| marker_name |
| Chisq | Chisq statistic | P< | Probability value calculated from chisq statistic |
Germplasm Population Distributions The following table is used for Chisq and TwoLetter Nucleotide and SSR. For SSR, the most frequent Allele pair is labelled as Homozygote 1, the second most frequent Allele pair is labelled as Homozygote 2 and the Heterozygote between the two Homozygotes is labelled Heterozygote.
Germplasm_type | Homozygote 1 ratio | Heterozygote ratio | Homozygote 2 ratio | RH | 0.5 | 0 | 0.5 | RIL | 0.5 | 0 | 0.5 | F2 | 0.25 | 0.5 | 0.25 | F3 | 0.375 | 0.25 | 0.375 | F4 | 0.4375 | 0.125 | 0.4375 | F5 | 0.46875 | 0.0625 | 0.46875 | F6 | 0.484375 | 0.03125 | 0.484375 | F7 | 0.4921875 | 0.015625 | 0.4921875 | F8 | 0.49609375 | 0.0078125 | 0.49609375 | F9 | 0.498046875 | 0.00390625 | 0.498046875 | BC1F1 | 0.5 | 0.5 | 0 | BC2F1 | 0.75 | 0.25 | 0 | BC3F1 | 0.875 | 0.125 | 0 | BC4F1 | 0.9375 | 0.0625 | 0 | BC5F1 | 0.96875 | 0.03125 | 0 | BC6F1 | 0.984375 | 0.015625 | 0 | BC7F1 | 0.9921875 | 0.0078125 | 0 | BC8F1 | 0.99609375 | 0.00390625 | 0 | BC1F2 | 0.625 | 0.25 | 0.125 | BC2F2 | 0.8125 | 0.125 | 0.0625 | BC3F2 | 0.90625 | 0.0625 | 0.03125 | BC4F2 | 0.953125 | 0.03125 | 0.015625 | BC5F2 | 0.9765625 | 0.015625 | 0.0078125 | BC6F2 | 0.98828125 | 0.0078125 | 0.00390625 | BC7F2 | 0.994140625 | 0.00390625 | 0.001953125 | BC8F2 | 0.997070313 | 0.001953125 | 0.000976563 | BC1F3 | 0.6875 | 0.125 | 0.1875 | BC2F3 | 0.84375 | 0.0625 | 0.09375 | BC3F3 | 0.921875 | 0.03125 | 0.046875 | BC4F3 | 0.9609375 | 0.015625 | 0.0234375 | BC5F3 | 0.98046875 | 0.0078125 | 0.01171875 | BC6F3 | 0.990234375 | 0.00390625 | 0.005859375 | BC7F3 | 0.995117188 | 0.001953125 | 0.002929688 | BC8F3 | 0.997558594 | 0.000976563 | 0.001464844 | BC1F4 | 0.71875 | 0.0625 | 0.21875 | BC2F4 | 0.859375 | 0.03125 | 0.109375 | BC3F4 | 0.9296875 | 0.015625 | 0.0546875 | BC4F4 | 0.96484375 | 0.0078125 | 0.02734375 | BC5F4 | 0.982421875 | 0.00390625 | 0.013671875 | BC6F4 | 0.991210938 | 0.001953125 | 0.006835938 | BC7F4 | 0.995605469 | 0.000976563 | 0.003417969 | BC8F4 | 0.997802734 | 0.000488281 | 0.001708984 | BC1F5 | 0.734375 | 0.03125 | 0.234375 | BC2F5 | 0.8671875 | 0.015625 | 0.1171875 | BC3F5 | 0.93359375 | 0.0078125 | 0.05859375 | BC4F5 | 0.966796875 | 0.00390625 | 0.029296875 | BC5F5 | 0.983398438 | 0.001953125 | 0.014648438 | BC6F5 | 0.991699219 | 0.000976563 | 0.007324219 | BC7F5 | 0.995849609 | 0.000488281 | 0.003662109 | BC8F5 | 0.997924805 | 0.000244141 | 0.001831055 | BC1F6 | 0.7421875 | 0.015625 | 0.2421875 | BC2F6 | 0.87109375 | 0.0078125 | 0.12109375 | BC3F6 | 0.935546875 | 0.00390625 | 0.060546875 | BC4F6 | 0.967773438 | 0.001953125 | 0.030273438 | BC5F6 | 0.983886719 | 0.000976563 | 0.015136719 | BC6F6 | 0.991943359 | 0.000488281 | 0.007568359 | BC7F6 | 0.99597168 | 0.000244141 | 0.00378418 | BC8F6 | 0.99798584 | 0.00012207 | 0.00189209 | BC1F7 | 0.74609375 | 0.0078125 | 0.24609375 | BC2F7 | 0.873046875 | 0.00390625 | 0.123046875 | BC3F7 | 0.936523438 | 0.001953125 | 0.061523438 | BC4F7 | 0.968261719 | 0.000976563 | 0.030761719 | BC5F7 | 0.984130859 | 0.000488281 | 0.015380859 | BC6F7 | 0.99206543 | 0.000244141 | 0.00769043 | BC7F7 | 0.996032715 | 0.00012207 | 0.003845215 | BC8F7 | 0.998016357 | 6.1E-05 | 0.001922607 | BC1F8 | 0.748046875 | 0.00390625 | 0.248046875 | BC2F8 | 0.874023438 | 0.001953125 | 0.124023438 | BC3F8 | 0.937011719 | 0.000976563 | 0.062011719 | BC4F8 | 0.968505859 | 0.000488281 | 0.031005859 | BC5F8 | 0.98425293 | 0.000244141 | 0.01550293 | BC6F8 | 0.992126465 | 0.00012207 | 0.007751465 | BC7F8 | 0.996063232 | 6.1E-05 | 0.003875732 | BC8F8 | 0.998031616 | 3.05E-05 | 0.001937866 |
Dominant Germplasm Type Distributions Dominant Nucleotide only. Two sets of statistics are calculated: Major-Pairing and Minor-Pairing.
Germplasm_type | Major-Pairing Major Allele ratio | Major-Pairing Minor Allele ratio | Minor-Pairing Major Allele ratio | Minor-Pairing Minor Allele ratio | RH | 0.5 | 0.5 | 0.5 | 0.5 | RIL | 0.5 | 0.5 | 0.5 | 0.5 | F2 | 0.75 | 0.25 | 0.25 | 0.75 | F3 | 0.625 | 0.375 | 0.375 | 0.625 | F4 | 0.5625 | 0.4375 | 0.4375 | 0.5625 | F5 | 0.53125 | 0.46875 | 0.46875 | 0.53125 | F6 | 0.515625 | 0.484375 | 0.484375 | 0.515625 | F7 | 0.5078125 | 0.4921875 | 0.4921875 | 0.5078125 | F8 | 0.50390625 | 0.49609375 | 0.49609375 | 0.50390625 | F9 | 0.501953125 | 0.498046875 | 0.498046875 | 0.501953125 | BC1F1 | 1 | 0 | 0.5 | 0.5 | BC2F1 | 1 | 0 | 0.75 | 0.25 | BC3F1 | 1 | 0 | 0.875 | 0.125 | BC4F1 | 1 | 0 | 0.9375 | 0.0625 | BC5F1 | 1 | 0 | 0.96875 | 0.03125 | BC6F1 | 1 | 0 | 0.984375 | 0.015625 | BC7F1 | 1 | 0 | 0.9921875 | 0.0078125 | BC8F1 | 1 | 0 | 0.99609375 | 0.00390625 | BC1F2 | 0.875 | 0.125 | 0.625 | 0.375 | BC2F2 | 0.9375 | 0.0625 | 0.8125 | 0.1875 | BC3F2 | 0.96875 | 0.03125 | 0.90625 | 0.09375 | BC4F2 | 0.984375 | 0.015625 | 0.953125 | 0.046875 | BC5F2 | 0.9921875 | 0.0078125 | 0.9765625 | 0.0234375 | BC6F2 | 0.99609375 | 0.00390625 | 0.98828125 | 0.01171875 | BC7F2 | 0.998046875 | 0.001953125 | 0.994140625 | 0.005859375 | BC8F2 | 0.999023438 | 0.000976563 | 0.997070313 | 0.002929688 | BC1F3 | 0.8125 | 0.1875 | 0.6875 | 0.3125 | BC2F3 | 0.90625 | 0.09375 | 0.84375 | 0.15625 | BC3F3 | 0.953125 | 0.046875 | 0.921875 | 0.078125 | BC4F3 | 0.9765625 | 0.0234375 | 0.9609375 | 0.0390625 | BC5F3 | 0.98828125 | 0.01171875 | 0.98046875 | 0.01953125 | BC6F3 | 0.994140625 | 0.005859375 | 0.990234375 | 0.009765625 | BC7F3 | 0.997070313 | 0.002929688 | 0.995117188 | 0.004882813 | BC8F3 | 0.998535156 | 0.001464844 | 0.997558594 | 0.002441406 | BC1F4 | 0.78125 | 0.21875 | 0.71875 | 0.28125 | BC2F4 | 0.890625 | 0.109375 | 0.859375 | 0.140625 | BC3F4 | 0.9453125 | 0.0546875 | 0.9296875 | 0.0703125 | BC4F4 | 0.97265625 | 0.02734375 | 0.96484375 | 0.03515625 | BC5F4 | 0.986328125 | 0.013671875 | 0.982421875 | 0.017578125 | BC6F4 | 0.993164063 | 0.006835938 | 0.991210938 | 0.008789063 | BC7F4 | 0.996582031 | 0.003417969 | 0.995605469 | 0.004394531 | BC8F4 | 0.998291016 | 0.001708984 | 0.997802734 | 0.002197266 | BC1F5 | 0.765625 | 0.234375 | 0.734375 | 0.265625 | BC2F5 | 0.8828125 | 0.1171875 | 0.8671875 | 0.1328125 | BC3F5 | 0.94140625 | 0.05859375 | 0.93359375 | 0.06640625 | BC4F5 | 0.970703125 | 0.029296875 | 0.966796875 | 0.033203125 | BC5F5 | 0.985351563 | 0.014648438 | 0.983398438 | 0.016601563 | BC6F5 | 0.992675781 | 0.007324219 | 0.991699219 | 0.008300781 | BC7F5 | 0.996337891 | 0.003662109 | 0.995849609 | 0.004150391 | BC8F5 | 0.998168945 | 0.001831055 | 0.997924805 | 0.002075195 | BC1F6 | 0.7578125 | 0.2421875 | 0.7421875 | 0.2578125 | BC2F6 | 0.87890625 | 0.12109375 | 0.87109375 | 0.12890625 | BC3F6 | 0.939453125 | 0.060546875 | 0.935546875 | 0.064453125 | BC4F6 | 0.969726563 | 0.030273438 | 0.967773438 | 0.032226563 | BC5F6 | 0.984863281 | 0.015136719 | 0.983886719 | 0.016113281 | BC6F6 | 0.992431641 | 0.007568359 | 0.991943359 | 0.008056641 | BC7F6 | 0.99621582 | 0.00378418 | 0.99597168 | 0.00402832 | BC8F6 | 0.99810791 | 0.00189209 | 0.99798584 | 0.00201416 | BC1F7 | 0.75390625 | 0.24609375 | 0.74609375 | 0.25390625 | BC2F7 | 0.876953125 | 0.123046875 | 0.873046875 | 0.126953125 | BC3F7 | 0.938476563 | 0.061523438 | 0.936523438 | 0.063476563 | BC4F7 | 0.969238281 | 0.030761719 | 0.968261719 | 0.031738281 | BC5F7 | 0.984619141 | 0.015380859 | 0.984130859 | 0.015869141 | BC6F7 | 0.99230957 | 0.00769043 | 0.99206543 | 0.00793457 | BC7F7 | 0.996154785 | 0.003845215 | 0.996032715 | 0.003967285 | BC8F7 | 0.998077393 | 0.001922607 | 0.998016357 | 0.001983643 | BC1F8 | 0.751953125 | 0.248046875 | 0.748046875 | 0.251953125 | BC2F8 | 0.875976563 | 0.124023438 | 0.874023438 | 0.125976563 | BC3F8 | 0.937988281 | 0.062011719 | 0.937011719 | 0.062988281 | BC4F8 | 0.968994141 | 0.031005859 | 0.968505859 | 0.031494141 | BC5F8 | 0.98449707 | 0.01550293 | 0.98425293 | 0.01574707 | BC6F8 | 0.992248535 | 0.007751465 | 0.992126465 | 0.007873535 | BC7F8 | 0.996124268 | 0.003875732 | 0.996063232 | 0.003936768 | BC8F8 | 0.998062134 | 0.001937866 | 0.998031616 | 0.001968384 |
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