TraceHaplotyper

This program genotypes a tracefile that results from sequencing of two chromosomes, which one of them having a deletion preceding a SNP. In such case the phase of these markers can be determined.
Example Data Set
Source code
uploaded_file1 -> Ga-gramd3-ex3f.ab1
uploaded_file2 -> Gramd3.exp
action -> phase

RESULTS

In the expected sequence the deletion is after base 89, indel size 1 bases.
SNP1 is at base 206, alleles C and A.
SNP2 is at base 262, alleles T and C.
In the trace file the deletion site detected at position 258, score 640.4 (lower than 600 may indicate low trace file quality)
hence, to align the expected and the trace sequences a 169-base difference is accounted for.
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Analysis for SNP1, alleles C and A
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Finding the SNP1 allele that is located on the Ins chromosome
The expected pair of bases before the SNP site is C A
In the trace, the pairs of bases are:
372 base1 A base2 G
373 base1 G base2 C
374 base1 A base2 C are in the expected SNP site
375 base1 A base2 C
376 base1 C base2 A
The pair of bases that should precede the site of SNP on the Ins chromosome was located at 1 bases from the expected position
hence, the site of SNP for the Ins chromosome is at position 375 base1 A base2 C of these the expected base for the Del chromosome is A
Haplotype 1 is: Del, C
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Finding the SNP1 allele that is located on the Del chromosome
The expected pair of bases before the SNP site is C A
In the trace, the pairs of bases are:
373 base1 G base2 C
374 base1 A base2 C
375 base1 A base2 C are in the expected SNP site
376 base1 C base2 A
377 base1 C base2 T
The pair of bases that should precede the site of SNP on the Del chromosome was located at 0 bases from the expected position
hence, the site of SNP for the Del chromosome is at position 375 base1 A base2 C of these the expected base for the Ins chromosome is C
Haplotype 2 is: Ins, A
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Analysis for SNP2, alleles T and C
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Finding the SNP2 allele that is located on the Ins chromosome
The expected pair of bases before the SNP site is G T
In the trace, the pairs of bases are:
428 base1 A base2 G
429 base1 A base2 G
430 base1 G base2 T are in the expected SNP site
431 base1 T base2 C
432 base1 A base2 T
The pair of bases that should precede the site of SNP on the Ins chromosome was located at 1 bases from the expected position
hence, the site of SNP for the Ins chromosome is at position 431 base1 T base2 C of these the expected base for the Del chromosome is T
Haplotype 1 is: Del, C
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Finding the SNP2 allele that is located on the Del chromosome
The expected pair of bases before the SNP site is C T
In the trace, the pairs of bases are:
429 base1 A base2 G
430 base1 G base2 T
431 base1 T base2 C are in the expected SNP site
432 base1 A base2 T
433 base1 T base2 A
The pair of bases that should precede the site of SNP on the Del chromosome was located at 1 bases from the expected position
hence, the site of SNP for the Del chromosome is at position 432 base1 A base2 T of these the expected base for the Ins chromosome is A
Haplotype 2 is: Ins, T
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/cowry_data/WEB.DIR/76620
View trace with ChromatogramApplet by Eugen Buehler
Eyal Seroussi Ph. D.

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