Founder Re-sequencing Data File (SRA051316.tar)

These are the raw data for the PE sequenced founders.  The files are all named A_B_C_fq.gz, where A is the library name, B is the replicate lane on the which the sample was run (libraries were run on several GAII lanes), and C is the F or R (1 or 2) read.  The libraries are numbered 1-18 and correspond to founder in the following manner (see King et al. Genome Research 2012 Table 1 for a mapping of founder names to populations). These fastq files are in the Illumina 1.5 format (not the Phred). 

my %foundernames = (1,'b1',2,'b3839',3,'b3841',4,'b3844',5,'b3846',6,'b3852',7,'b3864',8,'b3870',9,'b3875',10,'b3886',11,'t0',12,'t1',13,'t4',14,'t7',15,'SAM',16,'t0XSS',17,'t0XSAM',18,'b3841ST');

Libraries 1-15 are all highly inbred founders.  After the synthetic populations were long established we discovered that b3841 was segregating In(3R)Payne, and t0 was segregating In(2L)t -- both common cosmopolitan inversions.  We were able is isogenize b3841 for the standard re-arrangement, the sequence of this strain is b3841ST.  We were not able to isogenize t0 (apparently the inversion is a balanced lethal, every fly is a transheterozygote.  So we crossed t0 to both the sequenced strain (iso1) or SAM, selected offspring trans-heterozygotes for the standard arrangement, and sequenced the resulting F1 as libraries 16 and 17.  Using these two libraries we can infer the genotype of the standard chromosome of t0 for the large majority of SNPs (detailed in King et al. (Genome Research, 2012) and King et al. (Genetics, 2012).


RIL RAD Data File (SRA051306.tar)

All raw fastq files for the SE RADseq experiment associated with King et al (Genome Research 2012).  Once untarred the files all have the form A_B_C.fq.gz, where A is the RADseq library name, B is the RIL name, and C is the replicate lane a library was run on (some libraries were run across several GAII lanes, others a single HiSEQ2000 lane).  The RIL name is most often a 5 digit number, the first digit specifies the population (A=1, B=2), the second the replicate within the population, and the final 3 the RIL name.  But for many samples the RIL name is alphanumeric, and could specific a founder, the sequenced strain (as SeqS or iso1) -- these names could have "."'s in them.

RIL Re-sequencig Data File (RILSEQ4.tar)

Raw data for four fully re-sequenced (paired end) RILS. Filenames contain the RIL id and 1 for forward read or 2 for reverse read. Re-sequenced RILs include: 11027, 11067, 11100, 11152.