Release 4 includes a new Founder SNP table using BWA and GATK. The remaining tables are all identical to Release 3.
1) Founder SNP Table: Table of all SNPs in the DSPR founders.
Columns:
CHROM = ("X","2L","2R","3L","3R","4","U")
POS = integer position on chromosome using reference 5.x coordinates, 1st base = 1
REF = ("A", "C", "G", "T")
ALT = ("A", "C", "G", "T")
freqA1
N_A1
The above two columns are repeated for all founders (A1-A7, AB8, B1-B7). Founder A2 is given with the standard (inversion free) arrangement for 3R. B5 is given with the inferred standard arrangement from two crosses.
2) Founder TE Table: Table of all TEs in the DSPR founders
Chr = ("X","2L","2R","3L","3R","4","U")
Upstream = Upstream position
Downstream = Downstream position
Description = Type of TE (see Cridland et al. 2013. Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources. Molecular Biology and Evolution. 30(10): 2311-2327.)
15 columns of founder genotype IDs: A1-A7, AB8, B1-B7
3) RIL SNP Table: Table of all genotyped positions for all RILs in the DSPR.
Columns (There is no header row for this table. Columns are in the order listed here):
Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
RILID = ID number of RIL
Minor Allele = ("A", "C", "G", "T", "X"), X is a deletion relative to iso1
Major Allele = ("A", "C", "G", "T", "X"), X is a deletion relative to iso1
Minor Allele Count = Number of reads of the minor allele
Major Allele Count = Number of reads of the major allele
4) HMM Results for pA RILs (10 kb intervals): Table of results from the hidden Markov model for the pA RILs at regularly spaced 10kB positions.
Columns (There is no header row for this table. Columns are in the order listed here):
Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
RILID = ID number of RIL
36 columns of founder genotype probabilities:
[A1A1,A1A2,A1A3,A1A4,A1A5,A1A6,A1A7,A1A8,
A2A2,A2A3,A2A4,A2A5,A2A6,A2A7,A2A8,
A3A3,A3A4,A3A5,A3A6,A3A7,A3A8,
A4A4,A4A5,A4A6,A4A7,A4A8,
A5A5,A5A6,A5A7,A5A8,
A6A6,A6A7,A6A8,
A7A7,A7A8,
A8A8]
8 columns of additive probabilities:
["AA1", "AA2", "AA3", "AA4", "AA5", "AA6", "AA7", "AA8"]
5) HMM Results for pB RILs (10 kb intervals): Table of results from the hidden Markov model for the pB RILs at regularly spaced 10kB positions.
Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
RILID = ID number of RIL
36 columns of founder genotype probabilities:
[B1B1,B1B2,B1B3,B1B4,B1B5,B1B6,B1B7,B1B8,
B2B2,B2B3,B2B4,B2B5,B2B6,B2B7,B2B8,
B3B3,B3B4,B3B5,B3B6,B3B7,B3B8,
B4B4,B4B5,B4B6,B4B7,B4B8,
B5B5,B5B6,B5B7,B5B8,
B6B6,B6B7,B6B8,
B7B7,B7B8,
B8B8]
8 columns of additive probabilities:
["BB1", "BB2", "BB3", "BB4", "BB5", "BB6", "BB7", "BB8"]
6) HMM Results for pA RILs (RAD makers): Table of results from the hidden Markov model for the pA RILs at the RAD markers.
Columns (There is no header row for this table. Columns are in the order listed here):
Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
RILID = ID number of RIL
36 columns of founder genotype probabilities:
[A1A1,A1A2,A1A3,A1A4,A1A5,A1A6,A1A7,A1A8,
A2A2,A2A3,A2A4,A2A5,A2A6,A2A7,A2A8,
A3A3,A3A4,A3A5,A3A6,A3A7,A3A8,
A4A4,A4A5,A4A6,A4A7,A4A8,
A5A5,A5A6,A5A7,A5A8,
A6A6,A6A7,A6A8,
A7A7,A7A8,
A8A8]
8 columns of additive probabilities:
["AA1", "AA2", "AA3", "AA4", "AA5", "AA6", "AA7", "AA8"]
7) HMM Results for pB RILs (RAD markers): Table of results from the hidden Markov model for the pB RILs at the RAD markers.
Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
RILID = ID number of RIL
36 columns of founder genotype probabilities:
[B1B1,B1B2,B1B3,B1B4,B1B5,B1B6,B1B7,B1B8,
B2B2,B2B3,B2B4,B2B5,B2B6,B2B7,B2B8,
B3B3,B3B4,B3B5,B3B6,B3B7,B3B8,
B4B4,B4B5,B4B6,B4B7,B4B8,
B5B5,B5B6,B5B7,B5B8,
B6B6,B6B7,B6B8,
B7B7,B7B8,
B8B8]
8 columns of additive probabilities:
["BB1", "BB2", "BB3", "BB4", "BB5", "BB6", "BB7", "BB8"]
8) List of regularly spaced positions every 10kb.
Chr = ("X","2L","2R","3L","3R","4")
Ppos = integer position on chromosome using reference 5.x coordinates, 1st base = 0
Gpos = position in centiMorgans
Gaxis = position in cummulative centiMorgans with the chromosomes in the following sequence (X, 2, 3)