RGD QTLS readme file. Last updated - Oct 2014 contact: rgd.developers@mcw.edu In addition to QTLS_RAT and QTLS_HUMAN files, we are providing QTLS_MOUSE file. Mouse QTLs at RGD are downloaded from the Mouse Genome Informatics ftp site (http://www.informatics.jax.org/downloads/reports/index.html) on a weekly basis. We are providing qtl positions on current and older genomic maps, if available. The files are tab-delimited data, one row per QTL record. MAIN CHANGES: - Separate files for rat, human and mouse QTLS. - Separate columns for mapping data on the 3.4, 5.0 and 6.0 rat genome assemblies. - Additional columns specify the method of positioning of the QTL on the genome assembly (see below for details). - Columns specific to only one species are only included in that species' file. Leftmost columns are in common for both files. See below for specific information on column contents. - Within a tab delimited field multiple values are now separated by a semicolon ";" instead of a comma ",". This is to improve rendering of the files when viewed in Excel. - RATMAP_ID column is obsolete as of April 1, 2011 and it will be filled with blanks for compatibility - As of April 2013, rgd ids and symbol of crossed rat strains are given in separate columns, for easier sorting POSITIONING METHODS: A QTL is positioned on a genome assembly by using the flanking and peak markers as provided by the paper detailing the QTL. For each assembly there are four columns in the QTL file, e.g. for the rat 3.4 assembly: 3.4_MAP_POS_CHR - the chromosome, this may in rare cases, due to assembly differences, not match the chromosome given in the column "CHROMOSOME_FROM_REF" which is curated from the original paper. 3.4_MAP_POS_START - the start position, always for the + strand 3.4_MAP_POS_STOP - the stop position, always for the + strand 3.4_MAP_POS_METHOD - see below To be used a marker must map to exactly one location on a given assembly and be on the same chromosome as the other markers used for that QTL Ideally both flanking markers are used. If that is not possible a flank and a peak marker are used and the QTL is estimated to be symmetrical about the peak. If that is not possible the peak alone is used with an estimated QTL size about the peak (see below for information on size estimation). Finally if only one flank is available that is used with an estimated size extending from that flank (there may be directionality errors for this case as correct orientation can not be ensured in the absence of another marker). All estimates are bounded by the chromosome sizes. There is therefore a hierarchy of confidence in QTL position: 1 - by flanking markers 2 - by one flank and peak markers 3 - by peak only 4 - by one flank marker only 5 - by peak marker with size adjusted to avg qtl size for species 6 - position imported from external source Which method is used is listed in the column xxx_MAP_POS_METHOD. Users wishing the highest quality data may wish to filter only for case 1, or case 1 and 2. In the event that no position can be assigned to a QTL on a given assembly the positioning fields are left blank. QTL size estimates: Until such time as we have better methods to alternatively position uncertain markers the QTL size estimates used for "3 - by peak only" and "4 - by one flank marker only" are made from the global distribution of known QTL sizes for the given species. For human our current estimated QTL size is: 26 Mbp For mouse our current estimated QTL size is: 34 Mbp For rat our current estimated QTL size is: 45 Mbp COLUMN INFORMATION: First 25 columns in common between rat, mouse and human. For rat: #1 QTL_RGD_ID the RGD_ID of the QTL #2 SPECIES species name #3 QTL_SYMBOL official qtl symbol #4 QTL_NAME current qtl name #5 CHROMOSOME_FROM_REF the chromosome from the original paper #6 LOD maximum LOD score if given in paper #7 P_VALUE p-value for QTL if given in paper #8 VARIANCE variance if given in paper #9 FLANK_1_RGD_ID RGD_ID for flank marker 1, if in paper #10 FLANK_1_SYMBOL symbol for flank marker 1, if in paper #11 FLANK_2_RGD_ID RGD_ID for flank marker 2, if in paper #12 FLANK_2_SYMBOL symbol for flank marker 2, if in paper #13 PEAK_RGD_ID RGD_ID for peak marker, if in paper #14 PEAK_MARKER_SYMBOL symbol for peak marker, if in paper #15 TRAIT_NAME trait created for QTL #16 MEASUREMENT_TYPE measurement type for QTL #17 (UNUSED) #18 PHENOTYPES phenotype ontology annotation #19 ASSOCIATED_DISEASES diseases ontology annotation #20 CURATED_REF_RGD_ID RGD_ID of paper(s) on QTL #21 CURATED_REF_PUBMED_ID PUBMED_ID of paper(s) on QTL #22 CANDIDATE_GENE_RGD_IDS RGD_IDS for genes mentioned by paper author #23 CANDIDATE_GENE_SYMBOLS symbols for genes mentioned by paper author #24 INHERITANCE_TYPE dominant, recessive etc. #25 RELATED_QTLS symbols of related QTLS #26 (UNUSED) #27 5.0_MAP_POS_CHR chromosome for previous assembly 5.0 #28 5.0_MAP_POS_START start position for previous assembly 5.0 #29 5.0_MAP_POS_STOP stop position for previous assembly 5.0 #30 5.0_MAP_POS_METHOD qtl positioning method for previous assembly 5.0 #31 3.4_MAP_POS_CHR chromosome for old assembly 3.4 #32 3.4_MAP_POS_START start position for old assembly 3.4 #33 3.4_MAP_POS_STOP stop position for old assembly 3.4 #34 3.4_MAP_POS_METHOD qtl positioning method for old assembly 3.4 #35 CROSS_TYPE strain cross type #36 CROSS_PAIR pairing of strains for cross #37 STRAIN_RGD_ID1 RGD_ID of first strain crossed #38 STRAIN_RGD_ID2 RGD_ID of second strain crossed #39 STRAIN_RGD_SYMBOL1 symbol of first strain crossed #40 STRAIN_RGD_SYMBOL2 symbol of second strain crossed #41 6.0_MAP_POS_CHR chromosome for current assembly 6.0 #42 6.0_MAP_POS_START start position for current assembly 6.0 #43 6.0_MAP_POS_STOP stop position for current assembly 6.0 #44 6.0_MAP_POS_METHOD qtl positioning method for current assembly 6.0 #45 STRAIN_RGD_ID3 RGD_ID of third strain crossed #46 STRAIN_RGD_SYMBOL3 symbol of third strain crossed For mouse: #1 QTL_RGD_ID the RGD_ID of the QTL #2 SPECIES species name #3 QTL_SYMBOL official qtl symbol #4 QTL_NAME current qtl name #5 CHROMOSOME_FROM_REF the chromosome from the original paper #6 LOD maximum LOD score if given in paper #7 P_VALUE p-value for QTL if given in paper #8 VARIANCE variance if given in paper #9 FLANK_1_RGD_ID RGD_ID for flank marker 1, if in paper #10 FLANK_1_SYMBOL symbol for flank marker 1, if in paper #11 FLANK_2_RGD_ID RGD_ID for flank marker 2, if in paper #12 FLANK_2_SYMBOL symbol for flank marker 2, if in paper #13 PEAK_RGD_ID RGD_ID for peak marker, if in paper #14 PEAK_MARKER_SYMBOL symbol for peak marker, if in paper #15 TRAIT_NAME trait created for QTL #16 MEASUREMENT_TYPE measurement type for QTL #17 (UNUSED) #18 PHENOTYPES phenotype ontology annotation #19 ASSOCIATED_DISEASES diseases ontology annotation #20 CURATED_REF_RGD_ID RGD_ID of paper(s) on QTL #21 CURATED_REF_PUBMED_ID PUBMED_ID of paper(s) on QTL #22 CANDIDATE_GENE_RGD_IDS RGD_IDS for genes mentioned by paper author #23 CANDIDATE_GENE_SYMBOLS symbols for genes mentioned by paper author #24 INHERITANCE_TYPE dominant, recessive etc. #25 RELATED_QTLS symbols of related QTLS #26 MGI_ID MGI ID #27 37_MAP_POS_CHR chromosome for previous assembly 37 #28 37_MAP_POS_START start position for previous assembly 37 #29 37_MAP_POS_STOP stop position for previous assembly 37 #30 37_MAP_POS_METHOD qtl positioning method for previous assembly 37 #31 34_MAP_POS_CHR chromosome for old assembly 34 #32 34_MAP_POS_START start position for old assembly 34 #33 34_MAP_POS_STOP stop position for old assembly 34 #34 34_MAP_POS_METHOD qtl positioning method for old assembly 34 #35 CM_MAP_CHR chromosome on cM map #36 CM_MAP_POS absolute position on cM map #37 38_MAP_POS_CHR chromosome for current assembly 38 #38 38_MAP_POS_START start position for current assembly 38 #39 38_MAP_POS_STOP stop position for current assembly 38 #40 38_MAP_POS_METHOD qtl positioning method for current assembly 38 For human: #1 QTL_RGD_ID the RGD_ID of the QTL #2 SPECIES species name #3 QTL_SYMBOL official qtl symbol #4 QTL_NAME current qtl name #5 CHROMOSOME_FROM_REF the chromosome from the original paper #6 LOD maximum LOD score if given in paper #7 P_VALUE p-value for QTL if given in paper #8 VARIANCE variance if given in paper #9 FLANK_1_RGD_ID RGD_ID for flank marker 1, if in paper #10 FLANK_1_SYMBOL symbol for flank marker 1, if in paper #11 FLANK_2_RGD_ID RGD_ID for flank marker 2, if in paper #12 FLANK_2_SYMBOL symbol for flank marker 2, if in paper #13 PEAK_RGD_ID RGD_ID for peak marker, if in paper #14 PEAK_MARKER_SYMBOL symbol for peak marker, if in paper #15 TRAIT_NAME trait created for QTL #16 MEASUREMENT_TYP measurement type for QTL #17 (UNUSED) #18 PHENOTYPES phenotype ontology annotation #19 ASSOCIATED_DISEASES diseases ontology annotation #20 CURATED_REF_RGD_ID RGD_ID of paper(s) on QTL #21 CURATED_REF_PUBMED_ID PUBMED_ID of paper(s) on QTL #22 CANDIDATE_GENE_RGD_IDS RGD_IDS for genes mentioned by paper author #23 CANDIDATE_GENE_SYMBOLS symbols for genes mentioned by paper author #24 INHERITANCE_TYPE dominant, recessive etc. #25 RELATED_QTLS symbols of related QTLS #26 OMIM_ID OMIM ID #27 37_MAP_POS_CHR chromosome for current assembly 37 #28 37_MAP_POS_START start position for current assembly 37 #29 37_MAP_POS_STOP stop position for current assembly 37 #30 37_MAP_POS_METHOD qtl positioning method for current assembly 37 #31 36_MAP_POS_CHR chromosome for old assembly 36 #32 36_MAP_POS_START start position for old assembly 36 #33 36_MAP_POS_STOP stop position for old assembly 36 #34 36_MAP_POS_METHOD qtl positioning method for old assembly 36