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Notice removed Canonical answer required by everestial
Bounty Ended with Veedrac's answer chosen by everestial
Notice added Canonical answer required by everestial
Bounty Started worth 50 reputation by everestial
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301_Moved_Permanently
301_Moved_Permanently
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  tPossible
  transitions    ms02g_PG_al
P r ----  │       ┌┬┬┬ C|T
o a ||||  │       ││││ T|C
s n ||||  │       ││││ A|C
s s ||||  │       ││││ G|T
i i ||||  └─────> ││││  ×—————> Break Point
b t |||-          │││└ T|C
l i ||--          ││└─ T|C
e o |---          │└── T|C
  n ----         └─── T|A

  tPossible
  transitions    ms02g_PG_al
P r ----  │       ┌┬┬┬ C|T \
o a ||||  │       ││││ T|C | Block 1
s n ||||  │       ││││ A|C |
s s ||||  │       ││││ G|T /
i i ||||  └─────> ││││  ×—————> Break Point
b t |||-          │││└ T|C \
l i ||--          ││└─ T|C |
e o |---          │└── T|C | Block 2
  n ----         └─── T|A /
         | |
       ↓ ↓
    v v
        Hap A Hap B

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×—————> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×—————> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

  Possible
  transitions    ms02g_PG_al
    │       ┌┬┬┬ C|T
    │       ││││ T|C
    │       ││││ A|C
    │       ││││ G|T
    └─────> ││││  ×—————> Break Point
            │││└ T|C
            ││└─ T|C
            │└── T|C
            └─── T|A

  Possible
  transitions    ms02g_PG_al
    │       ┌┬┬┬ C|T \
    │       ││││ T|C | Block 1
    │       ││││ A|C |
    │       ││││ G|T /
    └─────> ││││  ×—————> Break Point
            │││└ T|C \
            ││└─ T|C |
            │└── T|C | Block 2
            └─── T|A /
                 ↓ ↓
             Hap A Hap B
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301_Moved_Permanently
301_Moved_Permanently
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ms02g_PI  ms02g_PG_al
6         C|T
6         T|C
6         A|C
6         G|T
×----------×----->×——————————×—————> Break Point
4         T|C
4         T|C
4         T|C
4         T|A

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×----->×—————> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×----->×—————> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

  Block-1-Hap-A with Block-2-Hap-B    vs.    Block-1-Hap-A with Block-2-Hap-A

  C|C × C|C × C|C × A|C = 0.58612            T|C × T|C × T|C × T|C = 0.000244
+ C|T × C|T × C|T × A|T = 0.3164           + T|T × T|T × T|T × T|T = 0.00391
+ C|A × C|A × C|A × A|A = 0.482            + T|A × T|A × T|A × T|A = 0.0007716
+ C|G × C|G × C|G × A|G = 0.3164           + T|G × T|G × T|G × T|G = 0.00391
                          ———————                                    —————————
                    Avg = 0.42523                              Avg = 0.002207

        Likelyhood Ratio = 0.42523 / 0.002207 = 192.67

ms02g_PI  ms02g_PG_al
6         C|T
6         T|C
6         A|C
6         G|T
×----------×-----> Break Point
4         T|C
4         T|C
4         T|C
4         T|A

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×-----> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×-----> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

ms02g_PI  ms02g_PG_al
6         C|T
6         T|C
6         A|C
6         G|T
×——————————×—————> Break Point
4         T|C
4         T|C
4         T|C
4         T|A

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×—————> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×—————> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

  Block-1-Hap-A with Block-2-Hap-B    vs.    Block-1-Hap-A with Block-2-Hap-A

  C|C × C|C × C|C × A|C = 0.58612            T|C × T|C × T|C × T|C = 0.000244
+ C|T × C|T × C|T × A|T = 0.3164           + T|T × T|T × T|T × T|T = 0.00391
+ C|A × C|A × C|A × A|A = 0.482            + T|A × T|A × T|A × T|A = 0.0007716
+ C|G × C|G × C|G × A|G = 0.3164           + T|G × T|G × T|G × T|G = 0.00391
                          ———————                                    —————————
                    Avg = 0.42523                              Avg = 0.002207

        Likelyhood Ratio = 0.42523 / 0.002207 = 192.67
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301_Moved_Permanently
301_Moved_Permanently
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chr  pos ms01e_PI    ms01e_PG_al ms02g_PI ms01e_PI  ms01e_PG_al ms02g_PG_al ms03g_PIms02g_PI  ms02g_PG_al  ms03g_PG_alms03g_PI ms04h_PI ms03g_PG_al  ms04h_PI ms04h_PG_al ms05h_PIms04h_PG_al  ms05h_PI  ms05h_PG_al ms06h_PI  ms06h_PI  ms06h_PG_al
2    15881764  4  4       C|T          6         C|T          7         T|T          7         T|T          7         C|T          7         C|T
2    15881767  4  4       C|C          6         T|C          7         C|C          7         C|C          7         T|C          7         C|C
2    15881989  4  4       C|C          6         A|C          7         C|C          7         C|C          7         A|T          7         A|C
2    15882091  4  4       G|T          6         G|T          7         T|A          7         A|A          7         A|T          7         A|C
2    15882451  4  4       C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|A
2    15882454  4  4       C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|T
2    15882493  4  4       C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|T
2    15882505  4  4       A|T          4         T|A          7         T|T          7         T|T          7         A|C          7         A|T

ms02g_PI  ms02g_PG_al
6         C|T
6         T|C
6         A|C
6         G|T
×----------×-----> Break Point
4         T|C
4         T|C
4         T|C
4         T|A

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×-----> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

enter image description here  

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×-----> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

calculating likelyhood

chr pos ms01e_PI    ms01e_PG_al ms02g_PI    ms02g_PG_al ms03g_PI    ms03g_PG_al ms04h_PI    ms04h_PG_al ms05h_PI    ms05h_PG_al ms06h_PI    ms06h_PG_al
2   15881764    4   C|T 6   C|T 7   T|T 7   T|T 7   C|T 7   C|T
2   15881767    4   C|C 6   T|C 7   C|C 7   C|C 7   T|C 7   C|C
2   15881989    4   C|C 6   A|C 7   C|C 7   C|C 7   A|T 7   A|C
2   15882091    4   G|T 6   G|T 7   T|A 7   A|A 7   A|T 7   A|C
2   15882451    4   C|T 4   T|C 7   T|T 7   T|T 7   C|T 7   C|A
2   15882454    4   C|T 4   T|C 7   T|T 7   T|T 7   C|T 7   C|T
2   15882493    4   C|T 4   T|C 7   T|T 7   T|T 7   C|T 7   C|T
2   15882505    4   A|T 4   T|A 7   T|T 7   T|T 7   A|C 7   A|T

enter image description here  calculating likelyhood

chr  pos       ms01e_PI  ms01e_PG_al  ms02g_PI  ms02g_PG_al  ms03g_PI  ms03g_PG_al  ms04h_PI  ms04h_PG_al  ms05h_PI  ms05h_PG_al  ms06h_PI  ms06h_PG_al
2    15881764  4         C|T          6         C|T          7         T|T          7         T|T          7         C|T          7         C|T
2    15881767  4         C|C          6         T|C          7         C|C          7         C|C          7         T|C          7         C|C
2    15881989  4         C|C          6         A|C          7         C|C          7         C|C          7         A|T          7         A|C
2    15882091  4         G|T          6         G|T          7         T|A          7         A|A          7         A|T          7         A|C
2    15882451  4         C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|A
2    15882454  4         C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|T
2    15882493  4         C|T          4         T|C          7         T|T          7         T|T          7         C|T          7         C|T
2    15882505  4         A|T          4         T|A          7         T|T          7         T|T          7         A|C          7         A|T

ms02g_PI  ms02g_PG_al
6         C|T
6         T|C
6         A|C
6         G|T
×----------×-----> Break Point
4         T|C
4         T|C
4         T|C
4         T|A

  t      ms02g_PG_al
P r ---- C|T
o a |||| T|C
s n |||| A|C
s s |||| G|T
i i ||||  ×-----> Break Point
b t |||- T|C
l i ||-- T|C
e o |--- T|C
  n ---- T|A

enter image description here

  t      ms02g_PG_al
P r ---- C|T \
o a |||| T|C | Block 1
s n |||| A|C |
s s |||| G|T /
i i ||||  ×-----> Break Point
b t |||- T|C \
l i ||-- T|C |
e o |--- T|C | Block 2
  n ---- T|A /
         | |
         v v
     Hap A Hap B

calculating likelyhood

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