Lettuce SFP Chip Project



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The Lettuce SPP Chip Project > Partners > Data > Experiment Info > Diversity Panel Analysis

The diversity panel analysis was carried out with the following filters on three replicates of 54 accessions including Salinas and Seriola (RIL population parents). The parents can be distinguished by their name SAL or SEL in the diversity panel. SAL_A or SAL_B correspond to two separate sets of CEL files, generated from three replicates each. Similarly SER_A and SER_B.

Fixed Filter Settings for Analysis
  1. Maximum frequency of major allele (A,B,C,D or -) = 95% (at least one rare allele in the entire panel)
  2. Maximum percentage of inconsistent genotype calls among 3 replications of each accession/line (haplotypes were called I when calls were AAB, BBA or AB- ) = 40%
  3. Maximum percentage of missing data (where all three chip replications returned missing value) = 95%
  4. Minimum number of valid probe at each position = 2%
Select Stringency Filter Settings
Minimum number of bases spanned by SPP = 4Minimum number of bases spanned by SPP = 2


Filter by Major Allele Frequency

Percentage of A<= %
Percentage of B<= %
Percentage of C<= %
Percentage of D<= %
Percentage of I<= %
Percentage of missing<= %





Choosing 10% of maximum inconsistent calls is enough to
retrieve more contigs containing SPP. If you go beyond I = 10%
your browser may not be able to support it and it may hang.
Select Retrieval Method

Select All Panel Accessions
This option will output a CSV file containing haplotypes for all accession analyzed.

Select Markers by Accession
This option can take from seconds to minutes depends on percentage
of inconsistent call .
Please do NOT hit the back button of your browser.
Accession:
Compare a Pair of Accessions
Retrieve polymorphic SPPs between any two selected accessions in the panel.
Accession1:
Accession2:
Select Markers by Contig Name for All Accesions
Please enter LettuceChip Contig
(e.g. CLS_S3_Contig2943).


Contig1:
Contig2:
Contig3:
Select Markers by Contig Name & Accesions
Please enter LettuceChip Contig
(e.g. CLS_S3_Contig2943).


Accession:
Contig1:
Contig2:
Contig3:

Print the results into a CSV file



Major Allele Frequency Definition:
The designation of final allele final calls in the haplotype table is based in the outcome of the three replication of chips per accession. Each two base position on the chip can
face one of the following situations.
For a bimodal distribution at each 2 base position on the chip the accessions with higher SFPdev ratio were assigned "A", with lower SFPdev values were assigned "B". If the SFPdev
value at a given position does not fall in the range of a bimodal distribution (A or B) it gets unassigned or (-).
Therefore at a given position:
  • If the three replications have the same value "A", "B" or "-" (AAA, BBB or ---), in the haplotype table they were assigned "A", "B" or "-", respectively.
  • If two of the replications are "A" and the third one is unassigned (AA-), the haplotype is "D" (not B).
  • If two of the replications are "B" and the third one is unassigned (BB-), the haplotype is "C" (not A).
  • If two replications return "A" and the third one return "B" (AAB), the haplotype call is "I" (Inconsistent).
  • If two replications return "B" and the third one return "A" (BBA), the haplotype call is "I" (Inconsistent).
  • If one replication returns "A", another one returns "B" and the third returns "-" (AB-), the haplotype call is "I" (Inconsistent).
    ("I" stands for inconsistency of the genotype calls at a given position)
Diversity Panel Analysis Related Files:


Contact information
Send Email to Hamid Ashrafi
Authors: Hans van Leeuwen, Hamid Ashrafi, Sebastian Reyes Chin-Wo


Last modified: February 06, 2016. 15:08:46 pm PST