MARKERS»SEARCH AVAILABLE FIELDS
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Information in the MARKERS Table
Marker
- This column is used for "internal" names or codes for a marker.
- For multiplex-readyTM markers, this code consists of a two-letter abbreviation for the cereal that the molecular marker has been developed for, followed by a four-digit number. "ta" indicates wheat markers, "hv" barley markers.
Published Name
- The published name of a marker is displayed in this column.
Chromosome
- If a marker has been mapped, the linkage group(s) it has been assigned to is (are) displayed in this column.
Prefix
- The prefix of the published marker name is found in this column.
Type
- Currently, the MARKERS Table can contain the following marker types:
- EST-SSR (microsatellite markers derived from expressed sequence tags)
- SSR (microsatellite markers)
- INDEL (insertion / deletion marker)
- STS (molecular marker derived from a sequence tagged site)
- DArT® (Diversity Arrays Technology marker, see also http://www.triticarte.com.au/)
- SNP (Single Nucleotide Polymorphism)
Quality
- This column can be used to provide informaton on a marker's quality. The marker quality scores assigned to multiplex-readyTM markers follow the system described in Stephenson et al. (1998) Theor Appl Genet 97, 946.
MQ Comments
- Additional comments about marker quality, if available.
Origin
- This column contains the name of the laboratory /publication where a marker was originally developed / described.
Range
- For multiplex-readyTM markers up to four allele size ranges are recorded, describing where to expect allele peaks and "noise" peaks when assessing domesticated wheat or barley germplasm with the marker. This information is used by binning software to construct multiplex-readyTM marker panels. Under "Range", the number of the allele size range that is displayed on that line in the MARKERS table is shown.
Start
- Allele size in base pairs at which an allele size range begins. Used by binning software to construct panels of multiplexTM markers.
Stop
- Allele size in base pairs at which an allele size range ends. Used by binning software to construct panels of multiplexTM markers.
Start 1 (2, 3, 4)
- Allele size in base pairs at which allele size range "1" ("2", "3", "4") begins. Used by binning software to construct panels of multiplexTM markers.
Stop 1 (2, 3, 4)
- Allele size in base pairs at which allele size range "1" ("2", "3", "4") ends. Used by binning software to construct panels of multiplexTM markers.
Forward Primer
- Sequence (5'→3') of forward locus-specific primer sequence.
Reverse Primer
- Sequence (5'→3') of reverse locus-specific primer sequence.
Opt Conc
- Optimal nanomolar primer concentration in multiplex-readyTM assay
Spatial Variant
- Some markers were re-engineered to create spatial variants by re-designing primers to bind to alternative target sites. Please be aware that a re-engineered marker may occasionally amplify different loci than the "original" marker it was based on. Data from a marker and its spatial variant cannot be automatically assumed to be comparable.
SV Comment
- Additional comments about spatial variants, if available.
Electrogram
- Link to an image file of a marker's typical allele profiles.
- For Wheat markers, the profiles on these images were created by assessing wheat cultivars (from top to bottom, with colour of trace in brackets):
Barunga (green), VPM6 Cook (blue), Chinese Spring (black), Gabo (red), M6 (green), Norin 10 (blue), Olympic (black) and Opata85 (red).
- For Barley markers, the electrogram profiles were created by assessing barley cultivars (from top to bottom, with colour of trace in brackets):
Alexis (green), Chebec (blue), Clipper (black), Harrington (red), Haruna Nijo (green), Sahara 3771 (blue), Sloop (black) and WI3 (red).
Marker Set
- This column contains the name of the 'GENica Marker Tools' marker set a marker belongs to. Please refer to the section on MARKER SETS for further information.
User Group
- This column displays the 'GENica Marker Tools' user group that a marker set was assigned to. Please also refer to the sections on MARKER SETS and on MY GROUPS for further information.
Dilution Factor
- Dilution factor that was applied to PCR product generated with an MRTTM marker before capillary separation to generate the attached electrogram image.
Desalt Method
- Desalt method used to clean up PCR product generated with an MRTTM marker before capillary separation to generate the attached electrogram image.
cM
- For mapped DArT® markers, its map location in centiMorgan on the Triticarte consensus maps for wheat and barley is listed here.
- For mapped barley SNP markers, map locations (in centiMorgan) are as shown on the SCRI barley SNP consensus map published by Rostoks et al. (2005: Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Molecular Genetics and Genomics 274:515-527)
Accession Number
- GenBank accession number, where available.
Putative Linkage
- Putative linkage of a marker to a known gene or QTL can be listed in this field.
Platform
- Technical platform on which a marker was implemented.
Species
- Common name for the species for which a marker was implemented.
Full Name
- Full name for the species for which a marker was implemented.
NCBI Taxonomy ID
Lab ID
- Internal name or code for a SNP marker.
SNP position
- Position (in base pair) where a SNP is found on a contig.
Contig
- Name of the contig on which a SNP is located.
LSP name
- Internal name or code given to the contig amplified with the "Locus-Specific Primer" (LSP) pair.
Forward LSP name
- Name of the forward "Locus-Specific Primer" (LSP) that is used to amplify a contig where a SNP is located.
Forward LSP
- Sequence (5'→3') of the forward "Locus-Specific Primer" (LSP) that is used to amplify a contig where a SNP is located.
Reverse LSP name
- Name of the reverse "Locus-Specific Primer" (LSP) that is used to amplify a contig where a SNP is located.
Reverse LSP
- Sequence (5'→3') of the reverse "Locus-Specific Primer" (LSP), that is used to amplify a contig where a SNP is located.
SNP1 name
- Name of the first of two probes used to assay a SNP, e.g. in OLA (oligonucleotide ligation assay) or ASPE (allele-specific primer extension) assays.
SNP1 sequence
- Sequence (5'→3') of the first of two probes used to assay a SNP, e.g. in OLA (oligonucleotide ligation assay) or ASPE (allele-specific primer extension) assays.
SNP1 LUA
- When SNPs are analysed on the Luminex platform in microsphere-based OLA or ASPE assays, this field gives the "FlexMAP tag" attached to the first of the two probes used to assay the SNP, abbreviated as "LUA (LUminex Array) number". E.g. "LUA10" refers to the "FlexMAP tag" with zip code number "10".
SNP1 allele
- SNP allele identified by the first of the two probes used to assay the SNP.
SNP2 name
- Name of the second of two probes used to assay a SNP, e.g. in OLA (oligonucleotide ligation assay) or ASPE (allele-specific primer extension) assays.
SNP2 sequence
- Sequence (5'→3') of the second of two probes used to assay a SNP, e.g. in OLA (oligonucleotide ligation assay) or ASPE (allele-specific primer extension) assays.
SNP2 LUA
- When SNPs are analysed on the Luminex platform in microsphere-based OLA or ASPE assays, this field gives the "FlexMAP tag" attached to the second of the two probes used to assay the SNP, abbreviated as "LUA (LUminex Array) number". E.g. "LUA10" refers to the "FlexMAP tag" with zip code number "10".
SNP2 allele
- SNP allele identified by the second of the two probes used to assay the SNP.
Access
- This field indicates whether access to the marker set that the marker belongs to was set to "private", "group" or "public". See also the section on MARKERS»SETS to read about marker sets and different access levels.
User Name
- Name of the user who imported the marker set that the marker belongs to.
excludedprobes
- List of SNPs that must not be multiplexed in a PCR-based assay with a SNP marker, as SNP probes are known to form dimers.
excludedcontigs
- List of contigs that must not be multiplexed in a PCR-based assay with a SNP marker, as SNP probes are known to anneal to these non-target contigs.
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