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["Additional data file 3. List of supercontigs where more than one marker was placed. The markers on the 16 supercontigs that do not show linkage (or close linkage) and on the 21 supercontigs that do show tight linkage are shown. "]
["The asterisk indicates the 24 intervals  that were used to obtain a direct estimate of recombination rate."]
[]
["locus","linkage group","physical distance between markers (bp)*","map distance (cM)",null,"order/comments"]
[null,null,"(used difference in microsat start position)"]
["16 incongruent scupercontigs"]
["SC0000000b","3-chr 2"]
["SC0000000c","4-chr 3",1002347,"unlinked"]
["SC0000001","3-chr 2",{"$nulls":3},"same linkage group but separated by 88 cM"]
["SC0000001b","3-chr 2",640375,88.755,null,"same linkage group but separated by 88 cM"]
["SC0000003","4-chr 3"]
["SC0000003b","3-chr 2",1582363,"unlinked"]
["SC0000007","2-chr Z"]
["SC0000007b","3-chr 2",2194777,"unlinked"]
["SC0000008","2-chr Z"]
["SC0000008c","1-chr 1",217410,"unlinked"]
["SC0000020","1-chr 1"]
["SC0000020b","6-chr 6",1218532,"unlinked"]
["SC0000023","3-chr 2"]
["SC0000023b","unlinked",648494,"unlinked"]
["SC0000030","1-chr 1"]
["SC0000030b","2-chr Z",804798,"unlinked"]
["SC0000071b","6-chr 6"]
["SC0000071c","5-chr 4",885269,"unlinked"]
["SC0000091b","2-chr Z",{"$nulls":3},"z-specific"]
["SC0000091c","7-chr 7",1597137,"unlinked",null,"autosomal"]
["SC0000119","3-chr 2"]
["SC0000119b","9-chr 5",650912,"unlinked"]
["SC0000123b","1-chr 1"]
["SC0000123c","4-chr 3",1362809,"unlinked"]
["SC0000146","6-chr 6",{"$nulls":3},"same linkage group but separated by ~34 cM"]
["SC0000146c","6-chr 6",521932,39.101,null,"same linkage group but separated by ~34 cM"]
["SC0000159b","5-chr 4"]
["SC0000159c","6-chr 6",1253092,"unlinked"]
["SC0000184","2-chr Z",{"$nulls":3},"no recomb w/sc184b, sc184 and sc184b were used in the analysis of recombination rate"]
["SC0000184b","2-chr Z",169194,0,"*","no recomb w/sc184,   sc184 and sc184b were used in the analysis of recombination rate"]
["SC0000184c","5-chr 4",608665,"unlinked"]
["SC0000195","2-chr Z",{"$nulls":3},"same linkage group but separated by 20 cM, pseduoautosomal"]
["SC0000195b","2-chr Z",1522324,20.687,null,"same linkage group but separated by 20 cM,  z-specific"]
[]
["21 congruent supercontigs"]
["SC0000005b","1-chr 1",{"$nulls":3},"physical order is the same as map order"]
["SC0000005","1-chr 1",1070822,4.795,"*","physical order is the same as map order"]
["SC0000005c","1-chr 1",1423890,11.729,"*","physical order is the same as map order"]
["SC0000005d","1-chr 1",867476,4.777,"*","physical order is the same as map order"]
["SC0000016","2-chr Z"]
["SC0000016b","2-chr Z",679706,0,"*"]
["SC0000018","5-chr 4"]
["SC0000018b","5-chr 4",1230287,5.836,"*"]
["SC0000021b","7-chr 7",{"$nulls":3},"physical order is the same as map order"]
["SC0000021c","7-chr 7",1573238,8.059,"*","physical order is the same as map order"]
["SC0000021d","7-chr 7",861047,5.548,"*","physical order is the same as map order"]
["SC0000024","2-chr Z"]
["SC0000024b","2-chr Z",933131,4.302,"*"]
["SC0000036","3-chr 2",{"$nulls":3},"not included in analysis of recombination rate because map distance between sc36 and sc152 not consistent with raw recombination between sc36b and sc36"]
["SC0000036b","3-chr 2",1016343,12.754,null,"not included in analysis of recombination rate because map distance between sc36 and sc152 not consistent with raw recombination between sc36b and sc36"]
["SC0000043","4-chr 3"]
["SC0000043b","4-chr 3",828844,6.749,"*"]
["SC0000055","2-chr Z"]
["SC0000055b","2-chr Z",757011,6.383,"*"]
["SC0000059","4-chr 3"]
["SC0000059b","4-chr 3",699082,4.471,"*"]
["SC0000063","5-chr 4",{"$nulls":3},"map distance between sc63b and sc236 was consistent with raw recombination between sc63 and sc63b, so included in analysis of recombination rate"]
["SC0000063b","5-chr 4",994990,4.529,"*","map distance between sc63b and sc236 was consistent with raw recombination between sc63 and sc63b, so included in analysis of recombination rate"]
["SC0000079b","4-chr 3"]
["SC0000079c","4-chr 3",1292389,1.437,"*"]
["SC0000085b","2-chr Z",{"$nulls":3},"map together in male meioses, not female (possible hot spot of recombination in female)"]
["SC0000085c","2-chr Z",1336882,10.524,"*","map together in male meioses, not female (possible hot spot of recombination in female)"]
["SC0000093","1-chr 1",{"$nulls":3},"map distance between sc93b and sc167 was consistent with raw recombination between sc93 and sc93b, so included in analysis of recombination rate"]
["SC0000093b","1-chr 1",1144746,1.168,"*","map distance between sc93b and sc167 was consistent with raw recombination between sc93 and sc93b, so included in analysis of recombination rate"]
["SC0000122","1-chr 1"]
["SC0000122b","1-chr 1",927247,1.284,"*"]
["SC0000130","5-chr 4"]
["SC0000130b","5-chr 4",1532568,4.099,"*"]
["SC0000153","1-chr 1"]
["SC0000153b","1-chr 1",692066,1.772,"*"]
["SC0000155","3-chr 2"]
["SC0000155b","3-chr 2",769598,0,"*"]
["SC0000304","4-chr 3"]
["SC0000304b","4-chr 3",468561,0,"*"]
["SC0000312","2-chr Z"]
["SC0000312b","2-chr Z",1344253,10.559,"*"]
["SC0000313","6-chr 6"]
["SC0000313b","6-chr 6",698451,1.931,"*"]
["SC0000685","4-chr 3"]
["SC0000685b","4-chr 3",415135,0,"*"]
[]
[]
["* The physical distance between markers indicates how far apart the markers designed on the same supercontig should be based on the base pair position of the start of the microsats."]
["For example, SC0b and SC0c should be ~1Mb apart, however, the genetic map showed no evidence of linkage between these markers, thus are considered incongruent."]