Columns for Supporting Table 2 (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 
Populotype = consensus call from samtools.  For all chromosome but 2L = A1-7,AB8,B1-7.  For chromosome 2L = A1-7,AB8,B1-B4,B5/iso1,B5/SAM,B6-7.
SNP = Among the non-N founders there are at least two base types segregating.
INDEL = Among the founders an "N" is segregating.
Non-synonymous SNP = Non-synonomous SNP or indel in a coding region

Columns for Supporting Table 3a (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 
FounderID = correspond to founder numbers in Supp Table 1 with the exception of B5XSS and B5XSAM which are crosses between B5 and iso1 and B5 and AB8 (Samarkand).  
("A1", "A2", "A3", "A4", "A5", "A6", "A7", "AB8", "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B5XSS", "B5XSAM")
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

Columns for Supporting Table 3b (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 

Columns for Supporting Table 4a (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"]

Columns for Supporting Table 4b (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: 
[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"] 

Supporting Table 6a contains phase matches for Q1-Q3
Supporting Table 6b contains phase matches for QR1-QR8
Columns for Supporting Table 6 (Header row follows the names listed here)

Chr = ("X","2L","2R","3L","3R","4")
Pos = integer position on chromosome using reference 5.x coordinates, 1st base = 0 
Populotype = consensus call from samtools.  For all chromosome but 2L = A1-7,AB8,B1-7.  For chromosome 2L = A1-7,AB8,B1-B4,B5/iso1,B5/SAM,B6-7.
EventFlavor = SNP, INDEL, non-synonymous SNP (NS)
QTL name = see Supporting Table 3

Supporting Table 7 contains ADH activity phenotype data
Columns for Supporting Table 7 (Header row follows the names listed here)

RILID = ID number of RIL
Nreps = number of replicates per RIL
ADHactivity.mean = mean ADH activity
ADHactivity.SD = standard deviation of ADH activity