An example SPAGeDi result file

example-spagedi-result.txt

SPAGeDi 1.4c (build 17-07-2013) - a program for Spatial Pattern Analysis of Genetic Diversity
               Written by Olivier Hardy & Xavier Vekemans
               Contributions by Reed Cartwright

Input file : "C:\Users\shau7031\AppData\Roaming\geneGIS\spagedi_data.txt"
Results file : "Z:\data\arcgis\addins\genegis\tests\data\tmxr.txt"
1318 individuals
2 categories: CA-OR, Cent_Am
Latitude-longitude coordinates (assumed to be in degrees; used to compute distances in km), Latitude, Longitude
14 loci: L_Ev1_1, L_Ev1_2, L_Ev104_1, L_Ev104_2, L_Ev14_1, L_Ev14_2, L_Ev21_1, L_Ev21_2, L_Ev37_1, L_Ev37_2, L_Ev94_1, L_Ev94_2, L_Ev96_1, L_Ev96_2
3 digits per allele
Max ploidy announced: 2
# indiv within each ploidy:  2x=165
  WARNING: There is(are) 1153 individual(s) without genotype at any locus

# groups (min - max # indiv per group): 
  2 categorical groups (184 - 1134)
  859 spatial groups (1 - 8)   WARNING: 543 groups with 1 indiv
  859 spatio-categorical groups (1 - 8)   WARNING: 543 groups with 1 indiv

GENE DIVERSITY and ALLELE FREQUENCIES
Locus	Population	Sample size	# missing genotypes (%)	# incomplete genotypes (%)	# of defined gene copies	NA: # alleles	NAe: Effective # alleles (Nielsen et al. 2003)	AR(k=62): Allelic richness (expected number of alleles among 62 gene copies)	He (gene diversity corrected for sample size, Nei 1978)	Fi (individual inbreeding coefficient)	h (gene diversity with UNORDERED alleles, Pons & Petit 1996)
Multilocus average												
Multilocus average	All populations confounded	1318	1180.1 (89.5%)	0.0 (0.0%)	275.7	7.93	4.04	6.73	0.6783	0.002	0.6741	
L_Ev1_1													L_Ev1_1 alleles:	123	125	127	129
L_Ev1_1	All populations confounded	1318	1243 (94.3%)	0 (0.0%)	150	4	2.09	3.07	0.5225	0.159	0.5224		frequency	0.473333	0.00666667	0.506667	0.0133333
L_Ev1_2													L_Ev1_2 alleles:	143	147	149	151	153
L_Ev1_2	All populations confounded	1318	1244 (94.4%)	0 (0.0%)	148	5	1.47	4.07	0.3189	0.068	0.3205		frequency	0.00675676	0.0540541	0.817568	0.108108	0.0135135
L_Ev104_1													L_Ev104_1 alleles:	131	133	135	137	139	141
L_Ev104_1	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	6	2.48	5.22	0.5971	-0.056	0.5831		frequency	0.59697	0.163636	0.030303	0.1	0.10303	0.00606061
L_Ev104_2													L_Ev104_2 alleles:	109	111	113	115	117	119
L_Ev104_2	All populations confounded	1318	1245 (94.5%)	0 (0.0%)	146	6	3.44	5.41	0.7097	-0.062	0.7079		frequency	0.109589	0.417808	0.0547945	0.308219	0.10274	0.00684932
L_Ev14_1													L_Ev14_1 alleles:	192	194	196	198	200	202	204	208	210	212	214	216	220
L_Ev14_1	All populations confounded	1318	1155 (87.6%)	0 (0.0%)	326	13	8.39	11.02	0.8809	-0.003	0.8824		frequency	0.0889571	0.00306748	0.0644172	0.202454	0.101227	0.122699	0.0214724	0.0981595	0.165644	0.0521472	0.0521472	0.00613497	0.0214724
L_Ev14_2													L_Ev14_2 alleles:	206	208	212	214	216	218
L_Ev14_2	All populations confounded	1318	1254 (95.1%)	0 (0.0%)	128	6	3.81	5.47	0.7375	0.090	0.7324		frequency	0.101563	0.046875	0.351563	0.320313	0.171875	0.0078125
L_Ev21_1													L_Ev21_1 alleles:	143	147	149	157	159	161	163	165	167	169
L_Ev21_1	All populations confounded	1318	1154 (87.6%)	0 (0.0%)	328	10	5.11	8.69	0.8044	-0.001	0.7978		frequency	0.0152439	0.0152439	0.0579268	0.112805	0.109756	0.192073	0.347561	0.10061	0.0396341	0.00914634
L_Ev21_2													L_Ev21_2 alleles:	147	155	159	175	179	183	187
L_Ev21_2	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	7	1.36	5.06	0.2648	0.039	0.2615		frequency	0.854545	0.0636364	0.0151515	0.0030303	0.0242424	0.0121212	0.0272727
L_Ev37_1													L_Ev37_1 alleles:	183	195	199	203	206	207	210	211	214	218	222	226	230
L_Ev37_1	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	13	6.18	10.47	0.8382	-0.041	0.8275		frequency	0.0030303	0.0848485	0.0363636	0.0636364	0.0151515	0.112121	0.0424242	0.00606061	0.318182	0.127273	0.130303	0.0515152	0.00909091
L_Ev37_2													L_Ev37_2 alleles:	100	104	106	108	110	112	114	116	118
L_Ev37_2	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	9	5.28	7.57	0.8104	0.013	0.8060		frequency	0.00909091	0.0515152	0.227273	0.124242	0.184848	0.1	0.0121212	0.278788	0.0121212
L_Ev94_1													L_Ev94_1 alleles:	109	111	113	115	117	119	121
L_Ev94_1	All populations confounded	1318	1155 (87.6%)	0 (0.0%)	326	7	3.39	6.31	0.7054	0.035	0.6960		frequency	0.0552147	0.159509	0.128834	0.48773	0.0644172	0.0981595	0.00613497
L_Ev94_2													L_Ev94_2 alleles:	137	143	145	147	149	151	153	155	157	159	161	163
L_Ev94_2	All populations confounded	1318	1154 (87.6%)	0 (0.0%)	328	12	5.99	9.92	0.8330	0.005	0.8318		frequency	0.0213415	0.0365854	0.0609756	0.0213415	0.17378	0.234756	0.234756	0.0335366	0.0152439	0.0182927	0.00304878	0.146341
L_Ev96_1													L_Ev96_1 alleles:	194	196	198	200	202	204	206
L_Ev96_1	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	7	3.93	6.39	0.7456	-0.008	0.7604		frequency	0.0212121	0.366667	0.0909091	0.0151515	0.0515152	0.287879	0.166667
L_Ev96_2													L_Ev96_2 alleles:	112	114	116	118	120	122
L_Ev96_2	All populations confounded	1318	1153 (87.5%)	0 (0.0%)	330	6	3.67	5.50	0.7278	-0.116	0.7082		frequency	0.193939	0.0393939	0.424242	0.148485	0.181818	0.0121212


VALUES OF THE COMPUTED STATISTICS
Genetic analyses at POPULATION level (1 pop = 1 CATEGORICAL GROUP -> 2 populations)
Dist classes						1
Max distance						4535.29
Number of pairs						1
% partic						100.0
CV partic						0.00
Mean distance						4535.29
Mean ln(distance)						8.41964

	Global F-statistics 					Pairwise Fst (ANOVA approach)		distance range for regression analyses
Locus	Fit	Fis	Fst			1		0-4535.29	b-lin(slope linear dist)	b-log(slope log dist)
ALL LOCI	0.0007	0.0024	-0.0016			-0.0016				
L_Ev1_1	0.1588	0.1588	-0.0000			-0.0000				
L_Ev1_2	0.0649	0.0715	-0.0070			-0.0070				
L_Ev104_1	-0.0571	-0.0551	-0.0019			-0.0019				
L_Ev104_2	-0.0658	-0.0583	-0.0071			-0.0071				
L_Ev14_1	-0.0008	-0.0042	0.0034			0.0034				
L_Ev14_2	0.0833	0.0959	-0.0140			-0.0140				
L_Ev21_1	-0.0002	-0.0009	0.0007			0.0007				
L_Ev21_2	0.0357	0.0406	-0.0051			-0.0051				
L_Ev37_1	-0.0430	-0.0404	-0.0025			-0.0025				
L_Ev37_2	0.0116	0.0137	-0.0021			-0.0021				
L_Ev94_1	0.0305	0.0370	-0.0067			-0.0067				
L_Ev94_2	0.0026	0.0056	-0.0031			-0.0031				
L_Ev96_1	-0.0089	-0.0075	-0.0014			-0.0014				
L_Ev96_2	-0.1036	-0.1236	0.0178			0.0178				
Jackknifed estimators (over loci)
Mean	0.0004	0.0020	-0.0016			-0.0016				
SE	0.0163	0.0174	0.0020			0.0020