Spreadsheet: b233dc60-42f4-4962-821c-bdc2eaf82bac
Sheet: Sheet1

Table1S: Raw data (allelic fractions) used to generate the haplotype for strain SC5314 | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6
Chr | unifier ID | SNP | Contig19 | YJB10700 | YJB10699 | YJB10698
ChR
RM | 3 | 1645/2358 | 19-10151 | 0.39 | 0.06 | 0.87
RM | 4 | 1261/2409 | 19-10190 | 0.4640128340862111 | 0.429883215501296 | 0.6048785552656559
RM | 12 | 1642/2179 | 19-10040 | 0.3574950193290962 | 0.2269611755667229 | 0.9597964800598882
RM | 2 | 1381/2345 | 19-10161 | 0.3522175170735498 | 0.0385118139350852 | 0.9856985512372409
RM | 1 | B13B19 | 19-10161 | 0.37 | 0.13 | 0.89
RK | 11 | 2270/2288 | 19-10148A | 0.5196060110830499 | 0.5566692281505259 | 0.85
RK | 10 | 1625/2453 | 19-10203A | 0.37 | 0.04 | 0.93
RK | 9 | 1458/2280 | 19-10203C | n.d. | 0.24 | 0.76
RK | 15 | 2083/2220 | 19-10053 | 0.3799095477661814 | 0.2078461952835098 | 0.98570584559179
RK | 13 | 1560/2471 | 19-10053 | 0.3685523266794381 | 0.06329501642273372 | 0.9740361402471152
RK | 6 | 1694/2254 | 19-10063 | 0.34 | 0.17 | 0.95
RK | 5 | 1477/2396 | 19-10193 | 0.31 | 0.03 | 0.98
RS,U | 45 | 1541/2137 | 19-10070A | 0.3432993798305554 | 0.126271966215952 | 0.9680463370467012
RS,U | 150 | 1891/2157 | 19-10147 | 0.4 | 0.29 | 0.72
RS,U | 20 | 2388/2421 | 19-10238 | 0.4174444603219952 | 0.2734680384413154 | 0.8197019649280313
RS,U | 19 | 2060/2400 | 19-10188 | 0.391556842942233 | 0.2430442753333294 | 0.9387127803601214
RS,U | 18 | 1772/2368 | 19-10057A | 0.33 | 0.05 | 0.98
RB2 | 16 | 1158/2429 | 19-10247 | 0.341555055794345 | 0.1043061712260498 | 0.983037251093864
Chr | unifier ID | SNP | Contig19 | RBY_9-3sm | 9318-1 | CAI4
Ch1
1S | 23 | 1799/2450 | 19-10237 | 0.9393617009403056 | 0.1562433843534657 | 0.351257465971086
1S | 22 | 1322/2294 | 19-10237 | 0.6597861254476873 | 0.0526173197649686 | 0.384115523465704
1S | 28 | 1449/2362 | 19-10173 | 0.5406922371344962 | 0.32 | n.d.
1S | 29 | 1363/2056 | 19-10186 | 0.5691376374489203 | 0.26 | 0.43
1S | 26 | 2281/2302 | 19-10163 | 0.6305209937355203 | 0.02 | 0.35
1S | 27 | 2032/2371 | 19-10163 | 0.6149130087408596 | 0.2440333194318542 | 0.4317889952017522
1S | 24 | MNS1 | 19-10087 | 0.6295636970722334 | 0.02 | 0.38
1S | 25 | 2036/2375 | 19-10087 | 0.6542907421340926 | 0.08 | 0.38
1S | 46 | 1584/2265 | 19-10073 | 0.6281147409771348 | 0.05239143904403919 | n.d.
1S | 8 | 1983/2203 | 19-10052 | 0.6177709001669821 | 0.1 | n.d.
1CC,1A | 41 | 2347/2406 | 19-10241 | 0.6716030728245733 | 0.04579196558515855 | n.d.
1B | 39 | CPH1 | 19-10205 | 0.6412735441313999 | 0.1665375360468438 | n.d.
1B | 38 | 2262/2275 | 19-10159 | 0.5938775122397988 | 0.19 | n.d.
1J | 33 | 1179/2238 | 19-10218 | 0.7092916491803876 | 0.02816602463597336 | 0.4497706563315119
1J | 32 | F12n4 | 19-10218 | 0.6665895766447608 | 0.13650181434026 | 0.3724618204885669
1J | 34 | 1794/2304 | 19-10215 | 0.6080268812465212 | 0.1816158705514387 | 0.412008281573499
1J | 35 | 1916/2198 | 19-10215 | 0.6587973740877255 | 0.07025339421832417 | 0.3295118627531117
1J | 36 | 1556/2491 | 19-10215 | 0.6102277141376572 | 0.04 | 0.36
1E | 30 | 1622/2428 | 19-10081 | 0.6296159776823852 | 0.0593940957328544 | n.d.
1L | 31 | 1361/2464 | 19-10064 | 0.6090239082558998 | n.d. | n.d.
1L | 147 | 2080/2297 | 19-10191 | 0.5606063893642781 | 0.3074004202416885 | 0.443856850586614
1L | 42 | 2106/2441 | 19-10216 | 0.6250950480838637 | 0.01660910205274455 | n.d.
1L | 43 | 1729/2211 | 19-10216 | 0.6332632567840422 | 0.03345517582457038 | n.d.
Chr | unifier ID | SNP | Contig19 | YJB10701 | CAI4 | CAI4-F3
Ch2
2U | 48 | 1353/2363 | 19-10139 | 0.2281295380493197 | 0.42 | 0.42
2U | 49 | 1551/2437 | 19-10139 | 0.02562975640602882 | 0.3781276121336151 | 0.3921043032218774
2U | 60 | 2051/2483 | 19-10119 | 0.2529373339156521 | 0.4180167583871966 | 0.4220501211280373
2U | 61 | 1517/2458 | 19-10119 | 0.06088602753823671 | 0.361549068425771 | 0.3559357965359305
2U | 58 | 2370/2467 | 19-10234 | 0.02230778421695463 | 0.3966282744451421 | 0.4034627268610087
2U | 57 | 1283/2296 | 19-10076 | 0.07557532147563606 | 0.42 | 0.37
2U | 56 | 1398/2125 | 19-10076 | 0.02841462041822129 | 0.36 | 0.34
2U | 55 | 2184/2321 | 19-10208 | 0.01483327140745927 | 0.41 | 0.41
2U | 63 | 1760/2185 | 19-10044 | 0.1397795267356945 | 0.3707259849486781 | 0.3606133828140541
2U | 59 | 1337/2356 | 19-10183 | 0.03908827931847692 | 0.32 | 0.32
2U | 64 | 1709/2474 | 19-10196A | 0.03066331419067847 | 0.34 | 0.36
2U | 51 | 2001/2434 | 19-10014 | 0.1642360321829218 | 0.3950155579931969 | 0.3815759811758672
2U | 54 | 1775/2077 | 19-10143 | 0.1515592953968943 | 0.43 | 0.42
2U | 53 | 1414/2481 | 19-10135 | 0.04299709211207629 | 0.3516859452694139 | 0.3277836692395201
2U | 52 | 2242/2334 | 19-10141 | 0.03091507941046601 | 0.38 | 0.36
2U | 65 | 1262/2474 | 19-10196B | 0.2664874963351911 | 0.43 | 0.4
2U | 66 | 2046/2319 | 19-10113 | 0.146154485342468 | 0.4 | 0.35
2U | 67 | 1600/2122 | 19-10125 | 0.1427022137357359 | 0.44 | 0.42
2U | 68 | 1314/2038 | 19-10125 | 0.08409326760184171 | 0.3515331937792074 | 0.3472404402375596
Chr | unifier ID | SNP | Contig19 | RBY_10-10 | RBY_E-9
Ch3
3P | 73 | 1423/2317 | 19-10227 | 0.03990352688230954 | 0.7732539344432894
3P | 44 | 2091/2447 | 19-10150 | 0.129993063009829 | 0.8834867850606178
3P | 76 | 2195/2207 | 19-10123 | 0.08502476674588375 | 0.8464419475655431
3P | 75 | 1848/2210 | 19-10123 | 0.06404881696849771 | 0.9474173098350215
3P | 74 | 1808/1882 | 19-10123 | 0.01846417553095835 | 0.9771701200687197
3P | 77 | 1629/1863 | 19-10046 | 0.07071921722760717 | 0.9712509573161964
3P | 78 | 2095/2215 | 19-10046 | 0.03640483833779613 | 0.9350932638669995
3P | 79 | 1838/2419 | 19-10046 | 0.3081566006901163 | 0.8539907718942028
3P | 80 | C18n1 | 19-10046 |  | 0.6809739991745769
3P | 81 | 1442/2490 | 19-10254 | 0.08682140011354553 | 0.9124688483871178
3O | 71 | 1765/2519 | 19-10236 | 0.1489159830998659 | 0.1059958532522207
Chr | unifier ID | SNP | Contig19 | RBY_E-6 | RBY_3-6 | RBY_10-3sm
Ch4
4N | 83 | 2346/2476 | 19-10231 | 0.04300821285303217 | 0.2913475964610818 | 0.6713996618774348
4N | 84 | 1335/2442 | 19-10200 | 0.04594558602320957 | 0.3830582327690034 | 0.6599104653900303
4N | 91 | 2309/2408 | 19-10212 | 0.1022932851145399 | 0.2631324087694933 | 0.6656379745756069
4N | 89 | 2004/2043 | 19-10212 | 0.06655649986965521 | 0.4842462186511001 | 0.7072384670723229
4N | 90 | 2101/2204 | 19-10212 | 0.1007061789898503 | 0.3991239185317264 | 0.5520987654320987
4N | 88 | 1881/2465 | 19-10158 | 0.09551820055783253 | 0.3576766209054822 | 0.6018799117409166
4N | 87 | 1644/2359 | 19-10158 | 0.3197625675093249 | 0.4259399251730617 | 0.6076868691874391
4N | 86 | 1685/2366 | 19-10158 | 0.02697520600723602 | 0.3736861559271356 | 0.6825053995680346
4N | 92 | 1826/2182 | 19-10174 | 0.01349916681835364 | 0.393443328759002 | 0.6435028248587571
4N | 85 | 2159/2205 | 19-10109 | 0.1809623721850279 | 0.4746992780755674 | 0.5756388161078412
4F2 | 70 | 1771/2510 | 19-10225 | 0.04703266614580166 | 0.2963182372125998 | 0.6257628207159911
4F2 | 93 | 1463/2009 | 19-10192 | 0.3968378319744939 | 0.4964776483691613 | 0.5007739775727131
4F2 | 94 | 2084/2131 | 19-10192 | 0.0225599845166766 | 0.3555791655414563 | 0.6377783121829996
4F2 | 96 | 2074/2337 | 19-10126 | 0.2726360009731703 | 0.4742741040451424 | 0.557577592878225
4H | 98 | 2145/2386 | 19-10104 | 0.01899930766656001 | 0.322478449466175 | 0.6446089165956203
4H | 97 | 2061/2424 | 19-10104 | 0.03720988666521789 | 0.3790729940376908 | 0.6551014173965997
4H | 95 | 1654/2166 | 19-10204 | 0.2271068155309026 | 0.4339048860335544 | 0.5770156194923335
4H | 99 | 1462/2445 | 19-10162 | 0.05170347710541229 | 0.3634514059912356 | 0.6952626080333081
4H | 101 | 2006/2431 | 19-10166 | 0.06095739365602815 | 0.3882832147845939 | 0.6798890211429052
4H | 100 | 1544/2477 | 19-10166 | 0.02805119209128018 | 0.3599168653178144 | 0.626663852087357
Chr | unifier ID | SNP | Contig19 | 4448 (MTLa) | 4449(MTLalpha)
Ch5
5M | 102 | 1855/2172 | 19-10080 | 0.18 | 0.7
5M | 109 | 1899/2008 | 19-10137 | 0.2578761834402616 | 0.8717581929154605
5M | 106 | SNF1 | 19-10137 | 0.1061409508418527 | 0.7376815504127376
5M | 103 | HST3 | 19-10137 | 0.09479964702435635 | 0.9557917122234711
5M | 110 | 1445/2395 | 19-10198 | 0.35 | 0.63
5M | 111 | 1922/2344 | 19-10170 | 0.3208322182512657 | 0.7740488536982789
5M | 112 | PDE1 | 19-10202 | 0.07 | 0.84
5M | 113 | 1969/2162 | 19-10202 | 0.1579204577866986 | 0.8695986868487066
5I | 114 | DPH5 | 19-10093 | 0.26 | 0.94
5I | 116 | 2093/2390 | 19-10194 | n.a. | 0.88
5I | 117 | 1817/2082 | 19-10194 | 0.0342811080669173 | 0.9666328528364667
5I | 118 | 1341/2493 | 19-10194 | 0.24355671237931 | 0.9225270043484902
5I | 120 | 2340/2493 | 19-10194 | 0.04 | 0.9
Chr | unifier ID | SNP | Contig19 | DKCa208 | RBY10-12
Ch6
6O | 121 | 2154/2381 | 19-10201 | 0.6392807963592722 | 0.1021165100467874
6O | 122 | 1578/2118 | 19-10035 | 0.6 | 0.101529478696558
6O | 124 | B15B20 | 19-10176 | 0.5879014589351476 | 0.07697304669652534
6O | 123 | 1534/2336 | 19-10181 | 0.6 | 0.1327185266445494
6O | 126 | 1735/2343 | 19-10230 | 0.61 | 0.07237848965514873
6O | 127 | 1870/2315 | 19-10230 | 0.65 | 0.04202180448975727
6O | 128 | 1395/2385 | 19-10230 | 0.6700170042052314 | 0.01341258129007229
6O | 129 | 1372/2355 | 19-10233 | 0.62 | 0.05972539748679462
6O | 130 | 1624/2448 | 19-10233 | 0.6852294450656305 | 0.04413000403317936
6C | 131 | 1466/1889 | 19-10031 | 0.4986178084755405 | 0.3908191353920532
6C | 132 | 2114/2404 | 19-10140 | 0.6964970424720262 | 0.02040928530630742
Chr | unifier ID | SNP | Contig19 | DKCa170 | RBY _9-3sm
Ch7
7F | 135 | YDL114 | 19-10248 | 0.4146207249046711 | 0.24248994603753
7F | 136 | YKL084 | 19-10248 | 0.072875749334519 | 0.09026586832225644
7F | 137 | 2397/2498 | 19-10248 | 0.1165445766050996 | 0.074402971686586
7G | 138 | RBP1 | 19-10187 | 0.36 | 0.06548760561137681
7G | 140 | YJL54 | 19-10219 | 0.39 | 0.1391701023775955
7G | 141 | 6.1345 | 19-10110 | 0.38 | 0.2300723131140994
7G | 144 | 6.282/2 | 19-10253 | 0.3617085238098645 | 0.06980805319788352