Results of data analysis
Performed on the 'USAFEL-UchiTelle-small.pop' file at: 


Population Summary
==================
Population Name: UchiTelle
       Lab code: USAFEL
  Typing method: 12th Workshop SSOP
      Ethnicity: Telle
      Continent: NW Asia
Collection site: Targen Village
       Latitude: 41 deg 12 min N
      Longitude: 94 deg 7 min E
        complex: 1


Population Totals
_________________
Sample Size (n): 10
Allele Count (2n): 20
Total loci in file: 3 [A, C, B]
Total loci with data: 3 [A, C, B]


Legend for all analyses
_______________________

    * = significant at the 5% level
   ** = significant at the 1% level
  *** = significant at the 0.1% level
 **** = significant at the 0.01% level
***** = significant at the 0.001% level
   

I. Single Locus Analyses
========================

1. Locus: A
___________

1.1. Allele Counts [A]
----------------------
Untyped individuals: 2.0
Sample Size (n): 8.0
Allele Count (2n): 16
Distinct alleles (k): 8

Counts ordered by frequency| Counts ordered by name     
Name     Frequency (Count) | Name     Frequency (Count) 
02:01    0.25000   4       | 01:01    0.06250   1       
32:04    0.18750   3       | 02:01    0.25000   4       
02:10    0.12500   2       | 02:10    0.12500   2       
03:01:02 0.12500   2       | 02:18    0.06250   1       
25:01    0.12500   2       | 03:01:02 0.12500   2       
01:01    0.06250   1       | 25:01    0.12500   2       
02:18    0.06250   1       | 32:04    0.18750   3       
68:14    0.06250   1       | 68:14    0.06250   1       
Total    1.00000   16      | Total    1.00000   16      


1.2. HardyWeinberg [A]
----------------------
Table of genotypes, format of each cell is: observed/expected.

   01:01   0/3e-2
   02:01    0/0.2    1/0.5
   02:10    0/0.1    0/0.5    0/0.1
   02:18   1/6e-2    0/0.2    0/0.1   0/3e-2
03:01:02    0/0.1    0/0.5    1/0.2    0/0.1    0/0.1
   25:01    0/0.1    1/0.5    0/0.2    0/0.1    0/0.2    0/0.1
   32:04    0/0.2    0/0.8    1/0.4    0/0.2    1/0.4    1/0.4    0/0.3
   68:14   0/6e-2    1/0.2    0/0.1   0/6e-2    0/0.1    0/0.1    0/0.2
            01:01    02:01    02:10    02:18 03:01:02    25:01    32:04
                             [Cols: 1 to 7]
   68:14   0/3e-2
            68:14
                             [Cols: 8 to 8]

                          Observed         Expected       Chi-square   DoF   p-value        
------------------------------------------------------------------------------------------
           Common No commmon genotypes; chi-square cannot be calculated

------------------------------------------------------------------------------------------
 Lumped genotypes Value not calculated.

------------------------------------------------------------------------------------------
  Common + lumped Value not calculated.

------------------------------------------------------------------------------------------
All heterozygotes                7             6.75             9e-3     1  0.9233           
------------------------------------------------------------------------------------------
Common heterozygotes by allele

------------------------------------------------------------------------------------------
Common genotypes
            Total                0             0.00
------------------------------------------------------------------------------------------


1.3. Guo and Thompson HardyWeinberg output (monte-carlo) [A]
------------------------------------------------------------
Steps in Monte-Carlo randomization: 100000
p-value (overall): 0.8115

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]


1.4. Slatkin's implementation of EW homozygosity test of neutrality [A]
-----------------------------------------------------------------------
Observed F: 0.1562, Expected F: 0.1886, Variance in F: 0.0013
Normalized deviate of F (Fnd): -0.9076, p-value of F: 0.2121


2. Locus: C
___________

2.1. Allele Counts [C]
----------------------
Untyped individuals: 0.0
Sample Size (n): 10.0
Allele Count (2n): 20
Distinct alleles (k): 9

Counts ordered by frequency| Counts ordered by name     
Name     Frequency (Count) | Name     Frequency (Count) 
01:02    0.20000   4       | 01:02    0.20000   4       
03:07    0.20000   4       | 02:10:06 0.10000   2       
02:10:06 0.10000   2       | 03:07    0.20000   4       
06:05    0.10000   2       | 06:05    0.10000   2       
07:12    0.10000   2       | 07:12    0.10000   2       
12:02    0.10000   2       | 08:04    0.05000   1       
15:07    0.10000   2       | 12:02    0.10000   2       
08:04    0.05000   1       | 15:07    0.10000   2       
18:01    0.05000   1       | 18:01    0.05000   1       
Total    1.00000   20      | Total    1.00000   20      


2.2. HardyWeinberg [C]
----------------------
Table of genotypes, format of each cell is: observed/expected.

   01:02    0/0.4
02:10:06    1/0.4    0/0.1
   03:07    0/0.8    0/0.4    1/0.4
   06:05    0/0.4    0/0.2    1/0.4    0/0.1
   07:12    2/0.4    0/0.2    0/0.4    0/0.2    0/0.1
   08:04    0/0.2    0/0.1    0/0.2    0/0.1    0/0.1   0/3e-2
   12:02    0/0.4    1/0.2    0/0.4    0/0.2    0/0.2    1/0.1    0/0.1
   15:07    0/0.4    0/0.2    1/0.4    1/0.2    0/0.2    0/0.1    0/0.2
   18:01    1/0.2    0/0.1    0/0.2    0/0.1    0/0.1   0/5e-2    0/0.1
            01:02 02:10:06    03:07    06:05    07:12    08:04    12:02
                             [Cols: 1 to 7]
   15:07    0/0.1
   18:01    0/0.1   0/3e-2
            15:07    18:01
                             [Cols: 8 to 9]

                          Observed         Expected       Chi-square   DoF   p-value        
------------------------------------------------------------------------------------------
           Common No commmon genotypes; chi-square cannot be calculated

------------------------------------------------------------------------------------------
 Lumped genotypes Value not calculated.

------------------------------------------------------------------------------------------
  Common + lumped Value not calculated.

------------------------------------------------------------------------------------------
All heterozygotes                9             8.65             0.01     1  0.9053           
------------------------------------------------------------------------------------------
Common heterozygotes by allele

------------------------------------------------------------------------------------------
Common genotypes
            Total                0             0.00
------------------------------------------------------------------------------------------


2.3. Guo and Thompson HardyWeinberg output (monte-carlo) [C]
------------------------------------------------------------
Steps in Monte-Carlo randomization: 100000
p-value (overall): 0.4779

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]
07:12+01:02 (2/0.400000) 0.0347* 0.0376*


2.4. Slatkin's implementation of EW homozygosity test of neutrality [C]
-----------------------------------------------------------------------
Observed F: 0.1350, Expected F: 0.1789, Variance in F: 0.0014
Normalized deviate of F (Fnd): -1.1641, p-value of F: 0.0668


3. Locus: B
___________

3.1. Allele Counts [B]
----------------------
Untyped individuals: 1.0
Sample Size (n): 9.0
Allele Count (2n): 18
Distinct alleles (k): 1

Counts ordered by freque| Counts ordered by name  
Name  Frequency (Count) | Name  Frequency (Count) 
13:01 1.00000   18      | 13:01 1.00000   18      
Total 1.00000   18      | Total 1.00000   18      

[Locus is monomorphic, so no further analyses performed]




II. Multi-locus Analyses
========================

Haplotype / linkage disequilibrium (LD) statistics
__________________________________________________

Pairwise LD estimates
---------------------
Locus pair            D      D'        Wn   ln(L_1)   ln(L_0)         S   ALD_1_2   ALD_2_1  permus p-value 
A:C             0.02579 0.86447   0.78174    -36.04    -55.27     38.45   0.76174   0.75337      99 0.2222 
A:B                  NA      NA        NA    -26.51    -26.51      0.00        NA        NA      99 0.1212 
C:B                  NA      NA        NA    -32.10    -32.10      0.00        NA        NA      99 0.0101*


Haplotype frequency est. for loci: A:C:B
----------------------------------------
Number of individuals: 10 (before-filtering)
Number of individuals: 8 (after-filtering)
Unique phenotypes: 8
Unique genotypes: 14
Number of haplotypes: 26
Loglikelihood under linkage equilibrium [ln(L_0)]: -55.268324
Loglikelihood obtained via the EM algorithm [ln(L_1)]: -36.043653
Number of iterations before convergence: 22

Haplotypes sorted by frequency        
haplotype                                 frequency# copies
02:10~01:02~13:01                         0.12500  2.0     
25:01~03:07~13:01                         0.12500  2.0     
03:01:02~07:12~13:01                      0.06250  1.0     
01:01~08:04~13:01                         0.06250  1.0     
02:18~12:02~13:01                         0.06250  1.0     
02:01~15:07~13:01                         0.06250  1.0     
32:04~18:01~13:01                         0.06250  1.0     
03:01:02~06:05~13:01                      0.06250  1.0     
32:04~15:07~13:01                         0.06250  1.0     
32:04~03:07~13:01                         0.06250  1.0     
02:01~01:02~13:01                         0.06250  1.0     
68:14~07:12~13:01                         0.06250  1.0     
02:01~02:10:06~13:01                      0.06250  1.0     
02:01~12:02~13:01                         0.06250  1.0     

Haplotypes sorted by name             
haplotype                                 frequency# copies
01:01~08:04~13:01                         0.06250  1.0     
02:01~01:02~13:01                         0.06250  1.0     
02:01~02:10:06~13:01                      0.06250  1.0     
02:01~12:02~13:01                         0.06250  1.0     
02:01~15:07~13:01                         0.06250  1.0     
02:10~01:02~13:01                         0.12500  2.0     
02:18~12:02~13:01                         0.06250  1.0     
03:01:02~06:05~13:01                      0.06250  1.0     
03:01:02~07:12~13:01                      0.06250  1.0     
25:01~03:07~13:01                         0.12500  2.0     
32:04~03:07~13:01                         0.06250  1.0     
32:04~15:07~13:01                         0.06250  1.0     
32:04~18:01~13:01                         0.06250  1.0     
68:14~07:12~13:01                         0.06250  1.0     



