ETLINK.OUT
ANNOTATED OUTPUT FROM ETLINK USING TEST.DAT FOR INPUT

  ETLINK: Linkage disequilibrium analysis

 plant data source 1/26/90

  No. isolates =   52   No. loci =   20

  Total no. alleles =     72


FOR THE FOLLOWING DISTRIBUTION, LEWONTIN'S (1964, GENETICS 49:49-67)
STANDARDIZED MEASURE OF LINKAGE DISEQUILIBRIUM, D', IS CALCULATED FOR
EACH PAIR OF ALLELES AT TWO LOCI AND THE FREQUENCY IS TABULATED OVER
ALL PAIRS OF LOCI.  D' RANGES FROM -1.0 TO +1.0.  FOR E.COLI POPULATIONS
THE DISTRIBUTION OF D' IS TYPICALLY U-SHAPED BECAUSE MOST PAIRS OF
ALLELES ARE IN COMPLETE ASSOCIATION (I.E. ONLY 3 OF THE POSSIBLE 4 HAPLO-
TYPES FOR 2 ALLELES AT LOCI ARE OBSERVED).  SEE HEDRICK AND THOMSON (1986,
GENETICS 112:135-156) FOR MORE INFORMATION ABOUT THIS MEASURE.

  Frequency distribution of D prime

    -1.0  1216.     .514
     -.9    27.     .011
     -.8    14.     .006
     -.7    22.     .009
     -.6    15.     .006
     -.5    21.     .009
     -.4    38.     .016
     -.3    19.     .008
     -.2    23.     .010
     -.1    34.     .014
      .0    18.     .008
      .1    25.     .011
      .2    44.     .019
      .3    27.     .011
      .4    31.     .013
      .5    44.     .019
      .6    23.     .010
      .7    25.     .011
      .8    24.     .010
      .9    17.     .007
     1.0   661.     .279

  Total no. comparisons =     2368     ALL PAIRS OF ALLELES AT TWO LOCI


THIS IS THE FREQUENCY DISTRIBUTION OF THE NUMBER OF MISMATCHES (I.E.
NUMBER OF LOCI WITH DIFFERENT ALLELES) IN COMPARISON OF THE ELECTRO-
MORPH PROFILES OF ALL PAIRS OF ISOLATES.  K IS THE NUMBER OF MISMATCHES,
N IS THE NUMBER OF ISOLATE-PAIRS OBSERVED THE DIFFER AT K LOCI, AND FREQ
IS THE RELATIVE FREQUENCY.  FOR M ISOLATES THERE ARE M*M PAIRWISE
COMPARISONS.

  Mismatch distribution

     k      n       freq
     0    178       .066
     1    224       .083
     2     86       .032
     3     36       .013
     4    112       .041
     5     96       .036
     6    224       .083
     7    310       .115
     8    460       .170  --  I.E. 460 PAIRS OF ISOLATES (17% OF ALL PAIRS)
     9    352       .130           DIFFER AT 8 LOCI
    10    346       .128
    11    162       .060
    12     72       .027
    13     34       .013
    14     12       .004
    15      0       .000
    16      0       .000
    17      0       .000
    18      0       .000
    19      0       .000
    20      0       .000


THE NEXT TABLE GIVES OBSERVED AND EXPECTED MOMENTS OF THE MISMATCH
DISTRIBUTION AS SHOWN IN TABLE 1 OF WHITTAM ET AL. (1983, PROC. NATL.
ACAD. SCI. 80:1751-1755).  THE CALCULATIONS FOLLOW THE METHODS OF BROWN
ET AL. (1980, GENETICS 96:523-536) WITH EXPECTED MOMENTS CALCULATED FROM
EQUATIONS 3-5 (PAGE 525), OBSERVED MOMENTS OBTAINED BY METHOD B (PAGE 529)
AND LOWER(L1) AND UPPER(L2) CONFIDENCE LIMITS FOR THE VARIANCE
ASSUMING INDEPENDENCE OF LOCI TABULATED BY EQUATION 23 (PAGE 530)

              OBSERVED   EXPECTED   INDEX
   Moments       M(i)      u(i)      X(i)  Ia = X(2)

     i = 2      11.927     3.211     2.714    VARIANCE
     i = 3     -25.183      .330   -77.297    3RD CENTRAL MOMENT
     i = 4     346.973    30.353    10.431    4TH CENTRAL MOMENT

    L1 =       1.970  L2 =    4.453  SE Ia =    .1933     95% CONFIDENCE LIMITS
SE IaIS THE STANDARD ERROR ON THE INDEX AS PRESENTED BY MAYNARD SMTIH
AND COWORKERS (1993, PROC. NATL. ACAD. SCI 90:4384)


QSTAR.OUT

ETLINK ALSO WRITES A FILE LISTING HEDRICK AND THOMSON Q* VALUES FOR
EACH PAIR OF LOCI.  Q* IS CALCULATED FROM HEDRICK AND THOMSON EQUATION 9
USING Q FROM EQUATION 8.  Q IS DISTRIBUTED APPROXIMATELY AS A CHI SQUARE
WITH DF DEGREES OF FREEDOM UNDER THE NULL HYPOTHESIS OF LINKAGE EQUILIBRIUM.