trouble understanding the in-del

[ashuchawla]

I have trouble understanding the following IN-DEL. I am not a Bioilogy person, more towards the informatics side of Bioinformatics and will highly appreciate if any one can explain to me where is the insertion/deletion in the following piece of code I picked up from NCBI-SNP database.



>gnl|dbSNP|rs157738182 rs=157738182|pos=256|len=511|taxid=1773|mol="genomic"|class=in-del|alleles="-/ACCGCCGAGCAGACCGCCATCCGCGAG"|build=135
GCCGAGAATC ACATGGACGC CCAACCGGCC GGCGACGCCA CCCCGACCCC GGCAACGGCG AAGCGGTCCC GGTCCCGCTC
ACCTCGTCGC GGGTCGACTC GGATGCGCAC CGTGCACGAA ACATCGGCTG GAGGGTTGGT CATTGACGGT ATCGACGGTC
CACGAGACGC GCAGGTCGCG GCTCTGATCG GCCGCGTCGA CCGGCGCGGC CGGCTGCTGT GGTCGCTACC CAAGGGGCAC
ATCGAGTTGG GCGAG
N
GTCGCCGAGG AGACCGGCAT CCGCGGCAGT GTGCTCGCCG CGCTGGGGCG CATCGACTAC TGGTTCGTCA CCGACGGCCG
GCGGGTGCAC AAGACCGTCC ACCATTATTT GATGCGGTTT TTAGGCGGAG AGCTGTCCGA CGAAGACCTC GAGGTAGCCG
AGGTAGCCTG GGTGCCGATC CGGGAACTGC CGTCTCGACT GGCCTACGCC GACGAACGTC GACTAGCCGA GGTGGCCGAC
GAACTGATCG ACAAG

[westerman]

I am not familiar with dbSNP but looking at the manual it clearly explains the fasta line.

ftp://ftp.ncbi.nih.gov/snp/00readme.txt

Basically the indel is at the N. The allele shows the non-insert sequence (-) on the left side of the slash and the insert sequence (ACC...GAG) on the other side.

[ashuchawla]

So I looked up the link you posted and I have below mentioned confusions:-
1. What do you mean by insert and non-insert sequences?
2. the link you posted shows the following format-
>gnl|dbSNP|rs271 rs=271|pos=51|len=101|taxid=9606|mol="Genomic"|class=1|alleles="G/A"|source="dbSNP"
5' sequence: CTGCATCACATGTACTGATTCTGTCCATTGGAACAGAGATGATGACTGGT
variation: R
3' sequence: TTACTAAACCCTGAGCCCTGGTGTTTCTGTTGATAGGGGGTTGCATTGAT

I am confused about the 5' and 3' sequence notations too. As far as I understand 'C' bonds with 'G' and 'A' with 'T' on complementary strands which is not the case here, then how are they in opposite directions?

I am not familiar with dbSNP but looking at the manual it clearly explains the fasta line.

ftp://ftp.ncbi.nih.gov/snp/00readme.txt

Basically the indel is at the N. The allele shows the non-insert sequence (-) on the left side of the slash and the insert sequence (ACC...GAG) on the other side.

[westerman]

1) One of your alleles does not have an insert. The other does. That is the definition on an indel.

2) The 5' and 3' sequences refer to the flanking sequences. Not the complimentary strands. In the case with the allele="G/A" [not your original sequence] but the one you referred to in message #3 then the two alleles will be 101 bases long and will look like:

#1) CTGCA...GGTGTTA...GAT
#2) CTCGA...GGTATTA...GAT

3) In your original sequence the alleles will look like

#1) GCCGA...CGAGGTCG...CAAG
#2) GCCGA...CGAGACCGCCGAGCAGACCGCCATCCGCGAGGTCG...CAAG

[ashuchawla]

Thanks a tonne for your help
I have Another question though , would you call the FASTA sequences I pasted above a paired end read?

1) One of your alleles does not have an insert. The other does. That is the definition on an indel.

2) The 5' and 3' sequences refer to the flanking sequences. Not the complimentary strands. In the case with the allele="G/A" [not your original sequence] but the one you referred to in message #3 then the two alleles will be 101 bases long and will look like:

#1) CTGCA...GGTGTTA...GAT
#2) CTCGA...GGTATTA...GAT

3) In your original sequence the alleles will look like

#1) GCCGA...CGAGGTCG...CAAG
#2) GCCGA...CGAGACCGCCGAGCAGACCGCCATCCGCGAGGTCG...CAAG