INSERT INTO t1 VALUES (469713,1,164123,1,164123,1),(317330,164124,317193,101,153170,1),(469434,317194,375620,101,58527,1),(591816,375621,484273,1,108653,1),(591807,484274,534671,91,50488,1),(318885,534672,649362,101,114791,1),(318728,649363,775520,102,126259,1),(336829,775521,813997,101,38577,1),(317740,813998,953227,101,139330,1),(1,813998,953227,101,139330,1);
CREATE TABLE t2 (
id int(10) unsigned NOT NULL default '0',
contig_id int(10) unsigned NOT NULL default '0',
seq_start int(10) NOT NULL default '0',
seq_end int(10) NOT NULL default '0',
strand tinyint(2) NOT NULL default '0',
KEY id (id)
);
INSERT INTO t2 VALUES (133195,469713,61327,61384,1),(133196,469713,64113,64387,1),(133197,1,1,1,0),(133197,1,1,1,-2);
SELECT e.id,
MIN( IF(sgp.raw_ori=1,
(e.seq_start+sgp.chr_start-sgp.raw_start),
(sgp.chr_start+sgp.raw_end-e.seq_end))) as start,
MAX( IF(sgp.raw_ori=1,
(e.seq_end+sgp.chr_start-sgp.raw_start),
(sgp.chr_start+sgp.raw_end-e.seq_start))) as end,
AVG(IF (sgp.raw_ori=1,e.strand,(-e.strand))) as chr_strand