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User Guide

 
 
Glossary
Align. depth (max.)
Number of aligned sequences in which a polymorphic allele (above quality threshold) could be identified. For SNP markers, the maximum align. depth is specified.
Assay information
Genotyping assay information, if available. PLP, RFLP, or TAMS assays.
Chrom.
Chromosome arm X, 2L, 2R, 3L, or 3R.
Coding information
If a SNP (marker) overlaps with a gene, corresponding information is given ('genic', 'intronic', 'exonic', 'FBgn').
Counter
Counter for current selection.
CS (Canton S)
Canton S wild type stocks, isogenized on one chromosome, respectively:
 
ChromosomeBloomington Stock
X#6364
2#6365
3#6366
Curated
'1' if SNP (marker) was visually inspected, otherwise '0'.
Cyt. region
Cytological location of the SNP. The reference table which correlates cytological bands with the reference genome sequence was provided by FlyBase.
EP (distal EP)
dEP stocks, which contain an EP element inserted at the distal end of the corresponding chromosome. Different EP stocks were used for each chromosome arm:
 
ChromosomeInserted ElementBloomington Stock
XEP1421#10277
2LEP511#6415
2REP755#6412
3LEP3104#6413
3REP381#6414
Exonic
'1' if SNP marker or SNP overlaps with an exon as annotated by FlyBase, Release 5.10; otherwise '0'.
FBgn
If SNP marker or SNP overlaps with a gene as annotated by FlyBase, Release 5.10, the corresponding FBgn is listed.
FR (proximal FRT)
FRT stocks, which contain an FRT element inserted at the proximal end of the corresponding chromosome. (Generated by Xu and Rubin, 1993.) Different FRT stocks were used for each chromosome arm:
 
ChromosomeInserted ElementBloomington Stock
XFRT19A#5579
2LFRT40A#5615
2RFRT42D#5616
3LFRT80B#5618
3RFRT82B#5619
Genic
'1' if SNP marker or SNP overlaps with a gene as annotated by FlyBase, Release 5.10; otherwise '0'.
Indel
A common form of polymorphism, consisting of a small insertion or deletion (typically only a few nucleotides long). Current maximum length: 360 bp.
Intronic
'1' if SNP marker or SNP overlaps with an intron as annotated by FlyBase, Release 5.10; otherwise '0'.
Left / Right flank
30nt sequence flanking the reference allele (Release 4), on 5- or 3-prime side.

Flanking sequences lie immediately 5-prime and 3-prime of SNP. Flanking sequences lie immediately 5-prime and 3-prime of SNP. If allele is '-' then position is the location of the last nt of the 5-prime flank.
Old ids
SNP marker or SNP ids as used in the first FLYSNPdb version.
OR (Oregon R)
Oregon R wild type stocks, isogenized on one chromosome, respectively:
 
ChromosomeBloomington Stock
X#6361
2#6362
3#6363
P_SNP
SNP probability score: The Bayesian posterior probability that a column of an alignment represents a polymorphic site, as opposed to a monomorphic site (A, C, G, or T). Calculated by the PolyBayes software.
Phred
Quality value of the base, calculated by the Phred software. Phred evaluates the trace surrounding each called base using four or five quality value parameters to quantify the trace quality. The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ), where P_e is the probability that the base call is an error. A quality value of, e.g., 30 means that the probability for the base call being an error is 10E-3 (0,001). (For more details see the Phred documentation.) The higher the PHRED value, the better is the trace quality, and the higher is the probability that the detected allele is true.
PLP (primer, seq., length)
PCR product length polymorphism assay for SNP genotyping. '1' if PLP assay has been verified, otherwise '0'. Created for >6nt long InDels, utilizing size differences between PCR products of the allelic variants. The genotype can be determined by separating PCR products on standard agarose gels. Typically, primers were designed so that PCR fragments are 130-230bp long for 7-20nt InDels, and 200-500bp for larger InDels. Primer sequences are indicated, if existing. Approximate PCR product lengths (bp) are also indicated.
Pos.1 / 2
Start and end of a SNP marker. Coordinates refer to Releases 3, 4, or 5, according to the user-specified selection.
Primer (seq.)
Primer names (sequences) for producing the SNP marker fragment (~1kb) by PCR.
Quality scores
For SNP markers: max. align. depth, max. stock count, curated. For SNP sites: Phred, P_SNP, align. depth, stock count, curated.
Rec.mar. (recessive markers)
Stocks containing recessive markers on the mapped chromosomes:
 
ChromosomeGenotypeBloomington Stock
Xsc[1] cv[1] v[1] f[1]#98
2al[1] b[1] c[1] sp[2]#210
3ru[1] h[1] th[1] st[1] cu[1] sr[1] e[s] ca[1]#576
Ref. (reference)
Drosophila melanogaster reference genome sequence. Available assembly versions: Release 3, 4, or 5. The stock used for obtaining the sequence was y[1] cn[1] bw[1] sp[1] (Bloomington #2057).
RFLP (enzymes)
Restriction fragment length polymorphism assay for SNP genotyping. '1' if RFLP assay has been predicted, otherwise '0'. If an RFLP site is predicted, a list of commercially available enzymes which cut differentially is specified.
SNP
Single nucleotide polymorphism. A (mostly) biallelic marker that can be used to distinguish two homologous chromosome regions of different origins. By definition, a SNP defines two alternative nucleotides that can occur at a specific site. The FLYSNP project uses an extended definition of SNPs which includes >1nt long polymorphisms and InDels. SNPs are specified by unique identifiers.
SNP marker
Set of closely linked SNPs, typically within an interval of ca. 1kb. A SNP marker may contain several SNPs. SNP markers are specified by unique identifiers.
SNP marker (old)
Names used in the first version of FLYSNPdb. The first 1-2 letters of the SNP marker name reflect the chromosome arm where the SNP marker is located.
SNP no. (old)
Names used in the first version of FLYSNPdb. The first 1-2 letters of the SNP marker name reflect the chromosome arm where the SNP marker is located.
SNP sites
Genomic site where a SNP was detected.
Stock count (max.)
Number of stocks from which genotype data is available. For SNP markers, the maximum stock count is specified.
TAMS
Tag-array minisequencing assay. '1' if existing and verified, otherwise '0'.
Total SNP count
Total number of SNPs found in this SNP marker.
Variant
Alleles observed in this SNP, in alphabetical order. '-' means deletion; '/' separates two alleles if they are >1nt long.
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How to use FLYSNPdb
 
Select Region
Select chromosome arm, Release (for coordinates), and molecular or cytological region. The latter two options are mutually exclusive.
Following options are possible: "position 1 - position 2" -> region between these two positions; "position 1 + region length (nt)" -> region between pos.1 and pos.1+region length (the latter option currently only available for 'molecular').
Examples: "100000 - 500000"; "100000 + 400000"; "21B - 21D".
For selecting SNPs from whole chromosome arms, leave the 'Location' field blank.
If you would like to download the search result as FlyBase GBrowse track file, please select the most recent genome version, Release 5.
Select Stocks
Up to five stocks were genotyped at each SNP site. Only the SNP(marker)s which are differential between Stock1 and Stock2 are listed. If alleles of all stocks should be listed, please select "all" for Stock1 and/or Stock2.
Summarized information about stocks used for SNP map creation:
name (abbr.)chrom. (arm)stock descriptionBloomington nr.map density (~kb)
Canton S (CS)Xwild type, isogenized on chrom. X#636450
Canton S (CS)2wild type, isogenized on chrom. 2#636550
Canton S (CS)3wild type, isogenized on chrom. 3#636650
Oregon R (OR)Xwild type, isogenized on chrom. X#6361100
Oregon R (OR)2wild type, isogenized on chrom. 2#636250
Oregon R (OR)3wild type, isogenized on chrom. 3#636350
recessive markers (Rec. mar.)Xsc[1] cv[1] v[1] f[1]#9850
recessive markers (Rec. mar.)2al[1] b[1] c[1] sp[2]#21050
recessive markers (Rec. mar.)3ru[1] h[1] th[1] st[1] cu[1] sr[1] e[s] ca[1]#57650
distal EP (EP)XEP1421#10277100
distal EP (EP)2LEP511#6415100
distal EP (EP)2REP755#6412100
distal EP (EP)3LEP3104#6413100
distal EP (EP)3REP381#6414100
proximal FR (FR)XFRT19A#557950
proximal FR (FR)2LFRT40A#5615100
proximal FR (FR)2RFRT42D#5616100
proximal FR (FR)3LFRT80B#5618100
proximal FR (FR)3RFRT82B#5619100
Select View
The 'SNP marker' table shows general information on the marker region, whereas the 'SNP sites' table contains more detailed data on each SNP. Only one type of view is selectable for each search.
Data concerning quality scores, genotyping assays, coding information (according Rel5.10) or old IDs are optionally available. One or multiple options can be selected.
Submit Search or Browse all
After selection of the above described options press 'Submit'.
Alternatively, the 'Browse all' button can be selected, which shows all SNP markers or SNPs. The 'View' options and the 'Release' choice are also valid for 'Browse all'.
Query Result
The query result can be downloaded as text file (see menu after pressing 'Download').
The 'Go to GBrowse' link leads to the FlyBase genome browser page for showing a graphical representation of the selected genomic region.
Create Sub-selection
Sub-selections within the query result can be made by either clicking on the checkboxes at the left side of each row, or by entering search terms in the empty boxes (fields) below each column. Multiple search criteria are possible (- resulting data will meet all criteria). Use '*' or '%' as wild card (in string searches, e.g. '*a*'), and '<' or '>' in queries for lower or higher numbers (e.g. '>10000'). After pressing 'Submit', a new query result page will open.
It is thus possible to specifically select Indels by either entering '*-' into the 'Variant' field (SNP sites view), or by writing '>0' in the 'Indel length' field.
Download Query Result
Search result tables can be downloaded as text files with either tabulators ('tab-separated'), commas ('comma-separated') or semicolons ('semi-colon-separated') as separators. It is also possible to download a FlyBase GBrowse track file containing the selected SNP marker or SNP site locations, which can be uploaded into GBrowse for graphical display. Please note that the genome browser shows the most recent assembly version, Release 5.
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