Mendelian HapMap
Previous  Next

Sometimes HapMap samples are included in Plates in order to serve as a control of the genotyping process. If a HapMap trio is included in a plate, it is possible to follow all Genotypes belonging to its Samples and check if mendelian inheritance rules are followed.

SNPator allows the user to do it automatically:

graphic

Options:

- Show All

Will include Cancelled genotypes in the Analysis

- Use single letter as homozigous

Haploid genotypes will be converted to homozygous diploid when performing the analysis.


Only trios presenting genotypes with the following number of alleles will be processed (2 stands for diploid, 1 for haploid and 0 for missing data):

Father
Mother
offspring
2
2
2
1
2
2
1
2
1
2
0
2
0
2
2


The resulting report will have 3 sections:

* A list of mendelian incompatibilities

-----------------------------------------------------------------
----------------------- Mendelian analysis ----------------------
-----------------------------------------------------------------

na07019 - snp01 : Mendelian incompatibility

   -> na07019 : GG
   -> na07022 (Father) : A
   -> na07056 (Mother) : GG

na07029 - snp01 : Mendelian incompatibility

   -> na07029 : G
   -> na06994 (Father) : G
   -> na07000 (Mother) : AA

* A list of instances excluded from the analysis

-----------------------------------------------------------------
---------------------------- Warnings ---------------------------
-----------------------------------------------------------------

na07029 - snp06 : Mendelian test not performed

   -> na07029 : T
   -> na06994 (Father) : T
   -> na07000 (Mother) :

na07048 - snp06 : Mendelian test not performed

   -> na07048 : T
   -> na07034 (Father) : T
   -> na07055 (Mother) :

* A list of all HapMap Samples included in the Plate. If a Sample is present in this section with no previous presence in the other two sections, it means that it has passed the Mendelian test correctly.


-----------------------------------------------------------------
----------------------- Processed samples -----------------------
-----------------------------------------------------------------

   -> NA06985
   -> NA06991
   -> NA06993
   -> NA06994
   -> NA07000
   -> NA07019
   -> NA07022
   -> NA07029
   -> NA07034
   -> NA07048
   -> NA07055
   -> NA07056