NaN in MLM output

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lccu...@gmail.com

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Apr 18, 2016, 8:22:04 AM4/18/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Hi everybody!

This is my first time using TASSEL, and I did an MLM analysis as described in the manual. However, when I check my output file, I notice that for most of my markers there is "NaN" in the columns add_effect, add_F, add_p, dom_effect and dom_p. Any idea why is this happening? My loci are polymorphic... I really appreciate if you can help me.

Thanks!

Laura

Peter Bradbury

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Apr 18, 2016, 8:59:20 AM4/18/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

MLM only decomposes the marker effect into additive and dominance components when there are three genotypes present. If the marker df = 1, then it only reports the marker main effect (which in this case is also the additive effect, since you cannot estimate a dominance effect).

Peter

lccu...@gmail.com

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Apr 19, 2016, 2:57:01 PM4/19/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Thanks for answering Peter!

I have another doubt regarding the p value in GLM: I am using TASSEL 5.0, and I get a column named "p" and other named "perm_p". Almost all the values in the perm_p are 1, so none of my markers are significant according to that column. That makes me wonder if I should use instead the p values in the column "p" (where I get significant loci).

Thanks in advance!

Laura

Fábio Pértille

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Jun 9, 2016, 4:54:41 PM6/9/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Hey Peter, I have the almost the same problem.

I am running two approaches, one comes from Affymetrix 600K Array, and this one, has the same results as the exposed situation here, df=1 NaN.

But, the second approach, is the CornellGBS results, and the most part of my SNP are polymorphic (df=3) but any value has marker effect, all of then are NaN

Can you help me?

Thank you:

Trait Marker Chr Pos df F p add_effect add_F add_p dom_effect dom_F dom_p error

df MarkerR2 Genetic Var Residual Var -2LnLikelihood

asa None 0 NaN NaN NaN NaN NaN NaN NaN NaN 444 NaN 159.9

5222 52.76017 3539.21457

asa S1_2187 1 2187 3 1.6414 0.17908 NaN NaN NaN NaN NaN NaN 444 0.01111 159.9

5222 52.76017 3539.21457

asa S1_2190 1 2190 3 1.06917 0.36188 NaN NaN NaN NaN NaN NaN 444 0.00724 159.9

5222 52.76017 3539.21457

asa S1_2193 1 2193 3 2.25054 0.08181 NaN NaN NaN NaN NaN NaN 444 0.01524 159.9

5222 52.76017 3539.21457

asa S1_2197 1 2197 3 2.43041 0.06464 NaN NaN NaN NaN NaN NaN 444 0.01645 159.9

5222 52.76017 3539.21457

...

I am running by Tassel 5 stand alone

Peter Bradbury

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Jun 9, 2016, 5:06:50 PM6/9/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

TASSEL MLM only attempts to decompose the genotype effect into additive and dominance components when there are there are exactly three genotype classes - two homozygous classes and a heterozygote class. That means you only get additive and dominance tests when df = 2.

Peter

Fábio Pértille

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Jun 9, 2016, 8:51:35 PM6/9/16

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The thing is... I cannot undestand why the program is considering df=3, if I only have 3 genotypes per SNP.
Do you know why?

rs#

alleles

chrom

pos

strand

assembly#

center

protLSID

assayLSID

panelLSID

QCcode

A01_762.CEL

A02_TT5989.CEL

A03_768.CEL

A03_788.CEL

A03_917.CEL

A04_1009.CEL

A04_1118.CEL

A05_1019.CEL

A05_1196.CEL

A05_1315.CEL

A06_1416.CEL

A06_1429.CEL

A06_1527.CEL

A07_1610.CEL

A07_1624.CEL

A07_1703.CEL

A08_1767.CEL

AX-75445978

A/G

33367

AX-75454925

T/C

37788

AX-75456096

G/A

38379

AX-75469048

A/G

44436

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Fábio Pértille

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Jun 9, 2016, 9:07:03 PM6/9/16

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Sorry, the last one is the affymetrix with df=2

the data with df=3 is this one:

rs#

alleles

chrom

pos

strand

assembly#

center

protLSID

assayLSID

panelLSID

QCcode

241:C3W34ACXX:3:Myplate02:A06

332:C3W34ACXX:3:Myplate02:B06

37:C3W34ACXX:3:Myplate02:G05

5649:C3W34ACXX:3:Myplate02:D06

5661:C3W34ACXX:3:Myplate02:E06

5921:C3W34ACXX:3:Myplate02:F06

6037:C3W34ACXX:3:Myplate02:G06

6232:C3W34ACXX:3:Myplate02:H06

886:C3W34ACXX:3:Myplate02:C06

88:C3W34ACXX:3:Myplate02:H05

F1-7716:C3W34ACXX:3:Myplate02:D05

F1-7810:C3W34ACXX:3:Myplate02:E05

F1-7978:C3W34ACXX:3:Myplate02:F05

F27765-1126:C4K6KACXX:6:Myplate10:D01

F27765-1127:C4K6KACXX:6:Myplate10:E01

F27765-1128:C4K6KACXX:6:Myplate10:F01

F27765-1129:C4K6KACXX:6:Myplate10:G01

F27765-1130:C4K6KACXX:6:Myplate10:H01

F27765-1324:C4K6KACXX:6:Myplate10:A02

F27765-1325:C4K6KACXX:6:Myplate10:B02

F27765-1326:C4K6KACXX:6:Myplate10:C02

F27765-1327:C4K6KACXX:6:Myplate10:D02

F27765-1328:C4K6KACXX:6:Myplate10:E02

F27765-1329:C4K6KACXX:6:Myplate10:F02

F27765-1330:C4K6KACXX:6:Myplate10:G02

F27765-1331:C4K6KACXX:6:Myplate10:H02

F27765-1332:C4K6KACXX:6:Myplate10:A03

F27765-1333:C4K6KACXX:6:Myplate10:B03

F27765-1536:C4K6KACXX:6:Myplate10:C03

F27765-1538:C4K6KACXX:6:Myplate10:D03

F27765-2047:C4K6KACXX:6:Myplate10:E03

F27765-2049:C4K6KACXX:6:Myplate10:F03

F27765-2050:C4K6KACXX:6:Myplate10:G03

F27765-2051:C4K6KACXX:6:Myplate10:H03

F27765-2052:C4JATACXX:4:Myplate09:A04

F27765-2215:C4JATACXX:4:Myplate09:B04

F27765-2216:C4JATACXX:4:Myplate09:C04

F27765-2217:C4JATACXX:4:Myplate09:D04

F27765-2218:C4JATACXX:4:Myplate09:E04

F27765-2219:C4JATACXX:4:Myplate09:F04

F27765-2220:C4JATACXX:4:Myplate09:G04

F27765-2221:C4JATACXX:4:Myplate09:H04

F27765-2222:C4JATACXX:4:Myplate09:A05

F27765-2223:C4JATACXX:4:Myplate09:B05

F27765-2224:C4JATACXX:4:Myplate09:C05

F27765-2382:C4JATACXX:4:Myplate09:D05

F27765-2383:C4JATACXX:4:Myplate09:E05

F27765-2384:C4JATACXX:4:Myplate09:F05

F27765-2385:C4JATACXX:4:Myplate09:G05

F27765-2386:C4JATACXX:4:Myplate09:H05

F27765-2387:C4JATACXX:4:Myplate09:A06

F27765-2388:C4JATACXX:4:Myplate09:B06

F27765-2538:C4JATACXX:4:Myplate09:C06

F27765-2539:C4JATACXX:4:Myplate09:D06

F27765-2540:C4JATACXX:4:Myplate09:E06

F27765-2541:C4JATACXX:4:Myplate09:F06

F27765-2542:C4JATACXX:4:Myplate09:G06

F27765-2543:C4JATACXX:4:Myplate09:H06

F27765-2545:C4JATACXX:4:Myplate09:A01

F27765-2546:C4JATACXX:4:Myplate09:B01

F27765-2547:C4JATACXX:4:Myplate09:C01

F27765-2548:C4JATACXX:4:Myplate09:D01

F27765-2549:C4JATACXX:4:Myplate09:E01

F27765-2550:C4JATACXX:4:Myplate09:F01

F27765-2688:C4JATACXX:4:Myplate09:G01

F27765-2689:C4JATACXX:4:Myplate09:H01

F27765-2690:C4JATACXX:4:Myplate09:A02

F27765-2691:C4JATACXX:4:Myplate09:B02

F27765-2692:C4JATACXX:4:Myplate09:C02

F27765-2693:C4JATACXX:4:Myplate09:D02

F27765-2694:C4JATACXX:4:Myplate09:E02

F27765-2740:C4JATACXX:4:Myplate09:F02

F27765-2741:C4JATACXX:4:Myplate09:G02

F27765-2742:C4JATACXX:4:Myplate09:H02

F27765-2743:C4JATACXX:4:Myplate09:A03

F27765-2744:C4JATACXX:4:Myplate09:B03

F27765-2797:C4JATACXX:4:Myplate09:C03

F27765-2798:C4JATACXX:4:Myplate09:D03

F27765-2799:C4K6KACXX:6:Myplate10:E03

F27765-2800:C4K6KACXX:6:Myplate10:F03

F27765-2801:C4K6KACXX:6:Myplate10:G03

F27765-2845:C4K6KACXX:6:Myplate10:H03

F27765-923:C4K6KACXX:6:Myplate10:A01

F27765-924:C4K6KACXX:6:Myplate10:B01

F27765-925:C4K6KACXX:6:Myplate10:C01

F27765:C4K6KACXX:6:Myplate10:H05

F27769:C4JATACXX:1:Myplate04:G06

F27810-0786:MERGE

F27810-0787:MERGE

F27810-0788:C54AMACXX:7:Myplate11:C01

F27810-0789:MERGE

F27810-0790:MERGE

F27810-0791:MERGE

F27810-0792:C54AMACXX:7:Myplate11:G01

F27810-0793:C54AMACXX:7:Myplate11:H01

F27810-0794:MERGE

F27810-1008:MERGE

F27810-1009:MERGE

F27810-1012:MERGE

F27810-1013:MERGE

F27810-1014:MERGE

F27810-1015:C54AMACXX:7:Myplate11:G02

F27810-1016:MERGE

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F27810-1215:MERGE

F27810-1429:MERGE

F27810-1430:MERGE

F27810-1431:MERGE

F27810-1432:MERGE

F27810-1433:C54AMACXX:7:Myplate11:G04

F27810-1434:MERGE

F27810-1435:MERGE

F27810-1623:MERGE

F27810-1624:MERGE

F27810-1625:MERGE

F27810-1626:MERGE

F27810-1783:MERGE

F27810-1784:MERGE

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F27810-1786:MERGE

F27810-1787:MERGE

F27810-1788:MERGE

F27810-1960:MERGE

F27810-2297:MERGE

F27810-2298:MERGE

F27810-2300:MERGE

F27810-2301:C3W34ACXX:3:Myplate02:A01

F27810-2302:C3W34ACXX:3:Myplate02:B01

F27810-2303:C3W34ACXX:3:Myplate02:C01

F27810-2459:C3W34ACXX:3:Myplate02:D01

F27810-2460:C3W34ACXX:3:Myplate02:E01

F27810-2461:C3W34ACXX:3:Myplate02:F01

F27810-2462:C3W34ACXX:3:Myplate02:G01

F27810-2463:C3W34ACXX:3:Myplate02:H01

F27810-2464:C3W34ACXX:3:Myplate02:A02

F27810-2465:C3W34ACXX:3:Myplate02:B02

F27810-2466:C3W34ACXX:3:Myplate02:C02

F27810-2617:C3W34ACXX:3:Myplate02:D02

F27810-2618:C3W34ACXX:3:Myplate02:E02

F27810-2619:C3W34ACXX:3:Myplate02:F02

F27810-2620:C3W34ACXX:3:Myplate02:G02

F27810-2621:C3W34ACXX:3:Myplate02:H02

F27810-2622:C3W34ACXX:3:Myplate02:A03

F27810-2720:C3W34ACXX:3:Myplate02:B03

F27810-2721:C3W34ACXX:3:Myplate02:C03

F27810-2722:C3W34ACXX:3:Myplate02:D03

F27810-2770:C3W34ACXX:3:Myplate02:E03

F27810-2902:C3W34ACXX:3:Myplate02:F03

F27810-2903:C3W34ACXX:3:Myplate02:G03

F27810-2904:C3W34ACXX:3:Myplate02:H03

F27810-2905:C3W34ACXX:3:Myplate02:A04

F27810-2906:C3W34ACXX:3:Myplate02:B04

F27810-2907:C3W34ACXX:3:Myplate02:C04

F27810-2924:C3W34ACXX:3:Myplate02:D04

F27810-2925:C3W34ACXX:3:Myplate02:E04

F27810-2927:C3W34ACXX:3:Myplate02:F04

F27810-2928:C3W34ACXX:3:Myplate02:G04

F27810-2929:C3W34ACXX:3:Myplate02:H04

F27810-2930:C3W34ACXX:3:Myplate02:A05

F27810-2931:C3W34ACXX:3:Myplate02:B05

F27810-2932:C3W34ACXX:3:Myplate02:C05

F27816-1043:C4JATACXX:1:Myplate04:B02

F27816-1044:C4JATACXX:1:Myplate04:C02

F27816-1045:C4JATACXX:1:Myplate04:D02

F27816-1046:C4JATACXX:1:Myplate04:E02

F27816-1047:C4JATACXX:1:Myplate04:F02

F27816-1048:C4JATACXX:1:Myplate04:G02

F27816-1049:C4JATACXX:1:Myplate04:H02

F27816-1050:C4JATACXX:1:Myplate04:A03

F27816-1051:C4JATACXX:1:Myplate04:B03

F27816-1052:C4JATACXX:1:Myplate04:C03

F27816-1053:C4JATACXX:1:Myplate04:D03

F27816-1239:C4JATACXX:1:Myplate04:E03

F27816-1240:C4JATACXX:1:Myplate04:F03

F27816-1241:C4JATACXX:1:Myplate04:G03

F27816-1242:C4JATACXX:1:Myplate04:H03

F27816-1243:C4DRPACXX:3:Myplate03:A01

F27816-1244:C4DRPACXX:3:Myplate03:B01

F27816-1245:C4DRPACXX:3:Myplate03:C01

F27816-1246:C4DRPACXX:3:Myplate03:D01

F27816-1247:C4DRPACXX:3:Myplate03:E01

F27816-1248:C4DRPACXX:3:Myplate03:F01

F27816-1249:C4DRPACXX:3:Myplate03:G01

F27816-1456:C4DRPACXX:3:Myplate03:H01

F27816-1458:C4DRPACXX:3:Myplate03:A02

F27816-1459:C4DRPACXX:3:Myplate03:B02

F27816-1460:C4DRPACXX:3:Myplate03:C02

F27816-1461:C4DRPACXX:3:Myplate03:D02

F27816-1462:C4DRPACXX:3:Myplate03:E02

F27816-1463:C4DRPACXX:3:Myplate03:F02

F27816-1465:C4DRPACXX:3:Myplate03:G02

F27816-1466:C4DRPACXX:3:Myplate03:H02

F27816-1649:C4DRPACXX:3:Myplate03:A03

F27816-1650:C4DRPACXX:3:Myplate03:B03

F27816-1651:C4DRPACXX:3:Myplate03:C03

F27816-1652:C4DRPACXX:3:Myplate03:D03

F27816-1653:C4DRPACXX:3:Myplate03:E03

F27816-1654:C4DRPACXX:3:Myplate03:F03

F27816-1655:C4DRPACXX:3:Myplate03:G03

F27816-1656:C4DRPACXX:3:Myplate03:H03

F27816-1804:C4DRPACXX:3:Myplate03:A04

F27816-1805:C4DRPACXX:3:Myplate03:B04

F27816-1806:C4DRPACXX:3:Myplate03:C04

F27816-1807:C4DRPACXX:3:Myplate03:D04

F27816-1809:C4DRPACXX:3:Myplate03:E04

F27816-1810:C4DRPACXX:3:Myplate03:F04

F27816-1811:C4DRPACXX:3:Myplate03:G04

F27816-1812:C4DRPACXX:3:Myplate03:H04

F27816-1813:C4DRPACXX:3:Myplate03:A05

F27816-1814:C4DRPACXX:3:Myplate03:B05

F27816-1981:C4DRPACXX:3:Myplate03:C05

F27816-1982:C4DRPACXX:3:Myplate03:D05

F27816-1983:C4DRPACXX:3:Myplate03:E05

F27816-1984:C4DRPACXX:3:Myplate03:F05

F27816-1985:C4DRPACXX:3:Myplate03:G05

F27816-1986:C4DRPACXX:3:Myplate03:H05

F27816-1988:C4DRPACXX:3:Myplate03:A06

F27816-1989:C4DRPACXX:3:Myplate03:B06

F27816-2145:C4DRPACXX:3:Myplate03:C06

F27816-2146:C4DRPACXX:3:Myplate03:D06

F27816-2147:C4DRPACXX:3:Myplate03:E06

F27816-2148:C4DRPACXX:3:Myplate03:F06

F27816-2149:C4DRPACXX:3:Myplate03:G06

F27816-2150:C4DRPACXX:3:Myplate03:H06

F27816-2151:C4JATACXX:1:Myplate04:A04

F27816-2152:C4JATACXX:1:Myplate04:B04

F27816-2153:C4JATACXX:1:Myplate04:C04

F27816-2316:C4JATACXX:1:Myplate04:D04

F27816-2317:C4JATACXX:1:Myplate04:E04

F27816-2318:C4JATACXX:1:Myplate04:F04

F27816-2319:C4JATACXX:1:Myplate04:G04

F27816-2320:C4JATACXX:1:Myplate04:H04

F27816-2321:C4JATACXX:1:Myplate04:A05

F27816-2322:C4JATACXX:1:Myplate04:B05

F27816-2323:C4JATACXX:1:Myplate04:C05

F27816-2324:C4JATACXX:1:Myplate04:D05

F27816-2481:C4JATACXX:1:Myplate04:E05

F27816-2482:C4JATACXX:1:Myplate04:F05

F27816-2483:C4JATACXX:1:Myplate04:G05

F27816-2484:C4JATACXX:1:Myplate04:H05

F27816-2485:C4JATACXX:1:Myplate04:A06

F27816-2634:C4JATACXX:1:Myplate04:B06

F27816-2635:C4JATACXX:1:Myplate04:C06

F27816-2636:C4JATACXX:1:Myplate04:D06

F27816-2638:C4JATACXX:1:Myplate04:E06

F27816-2639:C4JATACXX:1:Myplate04:F06

F27816-828:C4JATACXX:1:Myplate04:A01

F27816-829:C4JATACXX:1:Myplate04:B01

F27816-830:C4JATACXX:1:Myplate04:C01

F27816-831:C4JATACXX:1:Myplate04:D01

F27816-832:C4JATACXX:1:Myplate04:E01

F27816-833:C4JATACXX:1:Myplate04:F01

F27816-834:C4JATACXX:1:Myplate04:G01

F27816-835:C4JATACXX:1:Myplate04:H01

F27816-836:C4JATACXX:1:Myplate04:A02

F27816:C4JATACXX:1:Myplate04:H06

F27822:C4K6KACXX:6:Myplate10:G05

F27971-1116:C4JATACXX:2:Myplate07:D02

F27971-1117:C4JATACXX:2:Myplate07:E02

F27971-1118:C4JATACXX:2:Myplate07:F02

F27971-1119:C4JATACXX:2:Myplate07:G02

F27971-1120:C4JATACXX:2:Myplate07:H02

F27971-1121:C4JATACXX:2:Myplate07:A03

F27971-1122:C4JATACXX:2:Myplate07:B03

F27971-1123:C4JATACXX:2:Myplate07:C03

F27971-1124:C4JATACXX:2:Myplate07:D03

F27971-1125:C4JATACXX:2:Myplate07:E03

F27971-1315:C4JATACXX:2:Myplate07:F03

F27971-1316:C4JATACXX:2:Myplate07:G03

F27971-1317:C4JATACXX:2:Myplate07:H03

F27971-1318:C4JATACXX:2:Myplate07:A04

F27971-1319:C4JATACXX:2:Myplate07:B04

F27971-1320:C4JATACXX:2:Myplate07:C04

F27971-1321:C4JATACXX:2:Myplate07:D04

F27971-1322:C4JATACXX:2:Myplate07:E04

F27971-1323:C4JATACXX:2:Myplate07:F04

F27971-1527:C4JATACXX:2:Myplate07:G04

F27971-1528:C4JATACXX:2:Myplate07:H04

F27971-1529:C4JATACXX:2:Myplate07:A05

F27971-1531:C4JATACXX:2:Myplate07:B05

F27971-1532:C4JATACXX:2:Myplate07:C05

F27971-1533:C4JATACXX:2:Myplate07:D05

F27971-1534:C4JATACXX:2:Myplate07:E05

F27971-1703:C4JATACXX:2:Myplate07:G05

F27971-1704:C4JATACXX:2:Myplate07:H05

F27971-1705:C4JATACXX:2:Myplate07:A06

F27971-1706:C4JATACXX:2:Myplate07:B06

F27971-1707:C4JATACXX:2:Myplate07:C06

F27971-1865:C4JATACXX:2:Myplate07:D06

F27971-1866:C4JATACXX:2:Myplate07:E06

F27971-1867:C4JATACXX:2:Myplate07:F06

F27971-1868:C4JATACXX:2:Myplate07:G06

F27971-1869:C4JATACXX:2:Myplate07:H06

F27971-1870:C4JATACXX:3:Myplate08:A01

F27971-1871:C4JATACXX:3:Myplate08:B01

F27971-1872:C4JATACXX:3:Myplate08:C01

F27971-1873:C4JATACXX:3:Myplate08:D01

F27971-1874:C4JATACXX:3:Myplate08:E01

F27971-2041:C4JATACXX:3:Myplate08:F01

F27971-2042:C4JATACXX:3:Myplate08:G01

F27971-2043:C4JATACXX:3:Myplate08:H01

F27971-2044:C4JATACXX:3:Myplate08:A02

F27971-2045:C4JATACXX:3:Myplate08:B02

F27971-2046:C4JATACXX:3:Myplate08:C02

F27971-2208:C4JATACXX:3:Myplate08:D02

F27971-2209:C4JATACXX:3:Myplate08:E02

F27971-2210:C4JATACXX:3:Myplate08:F02

F27971-2212:C4JATACXX:3:Myplate08:G02

F27971-2213:C4JATACXX:3:Myplate08:H02

F27971-2214:C4JATACXX:3:Myplate08:A03

F27971-2372:C4JATACXX:3:Myplate08:B03

F27971-2373:C4JATACXX:3:Myplate08:C03

F27971-2374:C4JATACXX:3:Myplate08:D03

F27971-2375:C4JATACXX:3:Myplate08:E03

F27971-2376:C4JATACXX:3:Myplate08:F03

F27971-2377:C4JATACXX:3:Myplate08:G03

F27971-2378:C4JATACXX:3:Myplate08:H03

F27971-2379:C4JATACXX:3:Myplate08:A04

F27971-2380:C4JATACXX:3:Myplate08:B04

F27971-2381:C4JATACXX:3:Myplate08:C04

F27971-2529:C4JATACXX:3:Myplate08:D04

F27971-2530:C4JATACXX:3:Myplate08:E04

F27971-2531:C4JATACXX:3:Myplate08:F04

F27971-2532:C4JATACXX:3:Myplate08:G04

F27971-2533:C4JATACXX:3:Myplate08:H04

F27971-2534:C4JATACXX:3:Myplate08:A05

F27971-2535:C4JATACXX:3:Myplate08:B05

F27971-2536:C4JATACXX:3:Myplate08:C05

F27971-2537:C4JATACXX:3:Myplate08:D05

F27971-2682:C4JATACXX:3:Myplate08:E05

F27971-2683:C4JATACXX:3:Myplate08:F05

F27971-2684:C4JATACXX:3:Myplate08:G05

F27971-2685:C4JATACXX:3:Myplate08:H05

F27971-2686:C4JATACXX:3:Myplate08:A06

F27971-2687:C4JATACXX:3:Myplate08:B06

F27971-2732:C4JATACXX:3:Myplate08:C06

F27971-2733:C4JATACXX:3:Myplate08:D06

F27971-2734:C4JATACXX:3:Myplate08:E06

F27971-2735:C4JATACXX:3:Myplate08:F06

F27971-2736:C4JATACXX:3:Myplate08:G06

F27971-2737:C4JATACXX:3:Myplate08:H06

F27971-2738:C4K6KACXX:6:Myplate10:A05

F27971-2739:C4K6KACXX:6:Myplate10:B05

F27971-2792:C4K6KACXX:6:Myplate10:C05

F27971-2793:C4K6KACXX:6:Myplate10:D05

F27971-2795:C4K6KACXX:6:Myplate10:E05

F27971-912:C4JATACXX:2:Myplate07:A01

F27971-913:C4JATACXX:2:Myplate07:B01

F27971-914:C4JATACXX:2:Myplate07:C01

F27971-915:C4JATACXX:2:Myplate07:D01

F27971-916:C4JATACXX:2:Myplate07:E01

F27971-917:C4JATACXX:2:Myplate07:F01

F27971-918:C4JATACXX:2:Myplate07:G01

F27971-919:C4JATACXX:2:Myplate07:H01

F27971-920:C4JATACXX:2:Myplate07:A02

F27971-921:C4JATACXX:2:Myplate07:B02

F27971-922:C4JATACXX:2:Myplate07:C02

F27971:C4K6KACXX:6:Myplate10:F05

F27978-1189:C4K6KACXX:7:Myplate05:A03

F27978-1190:C4K6KACXX:7:Myplate05:B03

F27978-1191:C4K6KACXX:7:Myplate05:C03

F27978-1192:C4K6KACXX:7:Myplate05:D03

F27978-1193:C4K6KACXX:7:Myplate05:E03

F27978-1194:C4K6KACXX:7:Myplate05:F03

F27978-1195:C4K6KACXX:7:Myplate05:G03

F27978-1196:C4K6KACXX:7:Myplate05:H03

F27978-1197:C4K6KACXX:7:Myplate05:A04

F27978-1198:C4K6KACXX:7:Myplate05:B04

F27978-1199:C4K6KACXX:7:Myplate05:C04

F27978-1412:C4K6KACXX:7:Myplate05:D04

F27978-1413:C4K6KACXX:7:Myplate05:E04

F27978-1414:C4K6KACXX:7:Myplate05:F04

F27978-1415:C4K6KACXX:7:Myplate05:G04

F27978-1416:C4K6KACXX:7:Myplate05:H04

F27978-1417:C4K6KACXX:7:Myplate05:A05

F27978-1418:C4K6KACXX:7:Myplate05:B05

F27978-1419:C4K6KACXX:7:Myplate05:C05

F27978-1420:C4K6KACXX:7:Myplate05:D05

F27978-1607:C4K6KACXX:7:Myplate05:E05

F27978-1608:C4K6KACXX:7:Myplate05:F05

F27978-1609:C4K6KACXX:7:Myplate05:G05

F27978-1610:C4K6KACXX:7:Myplate05:H05

F27978-1611:C4K6KACXX:7:Myplate05:A06

F27978-1612:C4K6KACXX:7:Myplate05:B06

F27978-1613:C4K6KACXX:7:Myplate05:C06

F27978-1614:C4K6KACXX:7:Myplate05:D06

F27978-1615:C4K6KACXX:7:Myplate05:E06

F27978-1765:C4K6KACXX:7:Myplate05:F06

F27978-1766:C4K6KACXX:7:Myplate05:G06

F27978-1767:C4K6KACXX:7:Myplate05:H06

F27978-1768:C54AMACXX:6:Myplate06:A01

F27978-1769:C54AMACXX:6:Myplate06:B01

F27978-1770:C54AMACXX:6:Myplate06:C01

F27978-1771:C54AMACXX:6:Myplate06:D01

F27978-1772:C54AMACXX:6:Myplate06:E01

F27978-1773:C54AMACXX:6:Myplate06:F01

F27978-1774:C54AMACXX:6:Myplate06:G01

F27978-1943:C54AMACXX:6:Myplate06:H01

F27978-1944:C54AMACXX:6:Myplate06:A02

F27978-1945:C54AMACXX:6:Myplate06:B02

F27978-1946:C54AMACXX:6:Myplate06:C02

F27978-1947:C54AMACXX:6:Myplate06:D02

F27978-1948:C54AMACXX:6:Myplate06:E02

F27978-2114:C54AMACXX:6:Myplate06:F02

F27978-2115:C54AMACXX:6:Myplate06:G02

F27978-2116:C54AMACXX:6:Myplate06:H02

F27978-2117:C54AMACXX:6:Myplate06:A03

F27978-2118:C54AMACXX:6:Myplate06:B03

F27978-2119:C54AMACXX:6:Myplate06:C03

F27978-2280:C54AMACXX:6:Myplate06:D03

F27978-2281:C54AMACXX:6:Myplate06:E03

F27978-2282:C54AMACXX:6:Myplate06:F03

F27978-2283:C54AMACXX:6:Myplate06:G03

F27978-2284:C54AMACXX:6:Myplate06:H03

F27978-2285:C54AMACXX:6:Myplate06:A04

F27978-2286:C54AMACXX:6:Myplate06:B04

F27978-2444:C54AMACXX:6:Myplate06:C04

F27978-2445:C54AMACXX:6:Myplate06:D04

F27978-2446:C54AMACXX:6:Myplate06:E04

F27978-2447:C54AMACXX:6:Myplate06:F04

F27978-2448:C54AMACXX:6:Myplate06:G04

F27978-2449:C54AMACXX:6:Myplate06:H04

F27978-2450:C54AMACXX:6:Myplate06:A05

F27978-2451:C54AMACXX:6:Myplate06:B05

F27978-2602:C54AMACXX:6:Myplate06:C05

F27978-2603:C54AMACXX:6:Myplate06:D05

F27978-2604:C54AMACXX:6:Myplate06:E05

F27978-2605:C54AMACXX:6:Myplate06:F05

F27978-2606:C54AMACXX:6:Myplate06:G05

F27978-2607:C54AMACXX:6:Myplate06:H05

F27978-2608:C54AMACXX:6:Myplate06:A06

F27978-2767:C54AMACXX:6:Myplate06:B06

F27978-2768:C54AMACXX:6:Myplate06:C06

F27978-2769:C54AMACXX:6:Myplate06:D06

F27978-2830:C54AMACXX:6:Myplate06:E06

F27978-2872:C54AMACXX:6:Myplate06:F06

F27978-2873:C54AMACXX:6:Myplate06:G06

F27978-2874:C54AMACXX:6:Myplate06:H06

F27978-762:C4K6KACXX:7:Myplate05:A01

F27978-763:C4K6KACXX:7:Myplate05:B01

F27978-764:C4K6KACXX:7:Myplate05:C01

F27978-765:C4K6KACXX:7:Myplate05:D01

F27978-766:C4K6KACXX:7:Myplate05:E01

F27978-767:C4K6KACXX:7:Myplate05:F01

F27978-768:C4K6KACXX:7:Myplate05:G01

F27978-769:C4K6KACXX:7:Myplate05:H01

F27978-988:C4K6KACXX:7:Myplate05:A02

F27978-989:C4K6KACXX:7:Myplate05:B02

F27978-990:C4K6KACXX:7:Myplate05:C02

F27978-991:C4K6KACXX:7:Myplate05:D02

F27978-992:C4K6KACXX:7:Myplate05:E02

F27978-993:C4K6KACXX:7:Myplate05:F02

F27978-994:C4K6KACXX:7:Myplate05:G02

F27978-995:C4K6KACXX:7:Myplate05:H02

S1_2187

G/T

2187

S1_2190

T/C

2190

S1_2193

T/C

2193

CT	TC	TC	TC	CT	TT	TC	TC	TT
S1_2197	A/G	1	2197

S1_2205

T/A

2205

S1_2206

G/A

2206

...

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Fábio Pértille

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Jun 9, 2016, 9:16:30 PM6/9/16

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I am not sure about this, but looks like that I have some heterozygous like AG and GA, and the program is considering 3 df becouse I have two heterozygous

But, I don´t know why, because the data was generate by Tassel, and how can I change this.

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Peter Bradbury

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Jun 10, 2016, 9:34:41 AM6/10/16

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I have entered this as a bug in MLM but am not sure how quickly we will get it fixed. TASSEL does store AG and GA as different genotypes to provide a method for working with phased data. In the meantime, you can use the IUPAC ambiguity code for genotypes to get around the problem.

AA = A, GG = G, AG=Y, GA=Y, etc.

Peter

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Fábio Pértille

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Jun 10, 2016, 10:13:12 AM6/10/16

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Yes, It is solved.

Run the command in Tassel 5 stand alone using the hapmap.txt file exported without "Export as Diploids" option. You can unselect this option in a box that appear after you define the folder where you will export the hapmap file.
Thank you Peter.

Cheers, Fábio

Peter

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