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Archiver > GENEALOGY-DNA > 2005-09 > 1127938870


From: (John Chandler)
Subject: STR mutation rates
Date: Wed, 28 Sep 2005 16:21:10 -0400 (EDT)


Time for another update on mutation rates. I downloaded 2122
37-marker haplotypes from Ysearch, representing a mix of haplogroups,
and used the method described in the SMGF poster ASHG 2004-4, entitled
"Direct determination of mutation characteristics of Y chromosome STR
loci," to determine the mutation rates. However, I used the recently
augmented YHRD table of direct mutation-rate measurements from
father-son pairs as the calibration. I also converted the reported
SMGF rates to the same new calibration scale for comparison. Finally,
I computed the average rates for a variety of panels and tossed in the
corresponding panel averages announced by FTDNA at last year's
conference and the ones calculated from Charles Kerchner's log as of
now. Note: the multi-copy markers are shown here with the rate for
each copy assuming equipartition, and the panel averages are computed
by counting each copy as a separate marker.

Note the peculiarity of the log data: the average for 1-25 is higher
than either 1-12 or 13-25. This suggests a bias in the decisions to
upgrade from 12 to 25 -- those with observed mutations in a 12-marker
test were significantly more likely to upgrade than those with a 12/12
match. In particular, the average rate for the 12-marker tests of
those who upgraded is 0.00267, while the average for those who did
not upgrade is 0.00175. This effect would be even stronger if we
could count the 11/12 near-matches that exploded upon upgrade and
were therefore eliminated from the statistics.

John Chandler

----------------------------------------------------------------------
(This table is formatted to line up more-or-less correctly with both
proportional and fixed fonts.)

Locus ____ --SMGF_ASHG_2004-4--- ____ YSEARCH ____ FTDNA ____ K_Log
_____ ____ (poster) ____ (scale) ____ (scale)
385ab ____ 0.002800 ____ 0.00230 ____ 0.00217
388 ______ 0.000379 ____ 0.00031 ____ 0.00040
389i _____ 0.002184 ____ 0.00179 ____ 0.00179
389ii-i __ 0.002584 ____ 0.00212 ____ 0.00219
390 ______ 0.004405 ____ 0.00361 ____ 0.00370
391 ______ 0.003155 ____ 0.00259 ____ 0.00255
392 ______ 0.001488 ____ 0.00122 ____ 0.00136
393 ______ 0.001119 ____ 0.00092 ____ 0.00090
394 ______ 0.001548 ____ 0.00127 ____ 0.00123
426 ______ 0.000271 ____ 0.00022 ____ 0.00024
437 ______ 0.001755 ____ 0.00144 ____ 0.00144
438 ______ 0.001018 ____ 0.00084 ____ 0.00077
439 ______ 0.004181 ____ 0.00343 ____ 0.00349
441 ______ 0.001323 ____ 0.00109 ____ -------
442 ______ 0.003066 ____ 0.00252 ____ 0.00232
444 ______ 0.002956 ____ 0.00243 ____ -------
445 ______ 0.000952 ____ 0.00078 ____ -------
446 ______ 0.003143 ____ 0.00258 ____ -------
447 ______ 0.003891 ____ 0.00319 ____ 0.00308
448 ______ 0.002375 ____ 0.00195 ____ 0.00202
449 ______ 0.006464 ____ 0.00531 ____ 0.00574
452 ______ 0.001743 ____ 0.00143 ____ -------
454 ______ 0.000235 ____ 0.00019 ____ 0.00024
455 ______ 0.000312 ____ 0.00026 ____ 0.00032
456 ______ 0.005342 ____ 0.00439 ____ 0.00470
458 ______ 0.005804 ____ 0.00476 ____ 0.00484
459ab ____ 0.001176 ____ 0.00097 ____ 0.00091
460 ______ 0.002942 ____ 0.00241 ____ 0.00241
461 ______ 0.002327 ____ 0.00191 ____ -------
462 ______ 0.000532 ____ 0.00044 ____ -------
463 ______ 0.001623 ____ 0.00133 ____ -------
464abcd __ ------ * ____ ---- ** ____ 0.00279
570 ______ -------- ____ ------- ____ 0.00447
576 ______ -------- ____ ------- ____ 0.00549
607 ______ -------- ____ ------- ____ 0.00309
A10 ______ 0.003794 ____ 0.00311 ____ -------
C4 _______ 0.002355 ____ 0.00193 ____ -------
H4 _______ 0.003044 ____ 0.00250 ____ 0.00259
YCAIIab __ 0.001249 ____ 0.00102 ____ 0.00108
1B07 _____ 0.000925 ____ 0.00076 ____ -------
CDYab ____ -------- ____ ------- ____ 0.00672

Panels:
FT1-12 ___ 0.002242 ____ 0.00184 ____ 0.00185 ____ 0.00399 ___ 0.00245
FT13-25 __ 0.002860 ____ 0.00235 ____ 0.00236 ____ 0.00481 ___ 0.00256
FT1-25 ___ 0.002560 ____ 0.00210 ____ 0.00211 ____ 0.00441 ___ 0.00261
FT1-37 ___ -------- ____ ------- ____ 0.00255 ____ 0.00541 ___ 0.00450
RG26 _____ 0.002020 ____ 0.00166 ____ -------
RG43 _____ 0.002410 ____ 0.00198 ____ -------
Norway10__ 0.002245 ____ 0.00184 ____ 0.00185 ***
YHRD10 ___ 0.002530 ____ 0.00208 ____ 0.00208 ****

* Used 0.00350 for calculating panel averages.
** Used 0.00287 for calculating panel averages.
*** Panel of ten markers used in Norwegian father-son study, with a
measured average rate of 0.0020. (Dupuy et al. 2004).
**** Panel of ten markers with collected published (or almost
published) results, including the Norwegion study, but
not the same ten markers.


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