progress:2008[The mtDNA H Haplogroup Project] 

The mtDNA H Haplogroup Project
 

Introduction

When using mtDNA to further our genealogical research, we usually have two goals. The first is to prove or add to the substance of our proof that our particular ancestor was the daughter in a family. Lost to history through marriage, destroyed records, and failure to be recorded in public documents, we are lucky to find supporting evidence. If there are land records and wills we may be able to build a case for preponderance-of-evidence as proof of a relationship. It is more likely though that we will reach a brick wall where our ancestress is a woman traveling with her small children to join her husband or an eleven year old child in the census who is living with a family that she was not with in the prior census. mtDNA provides us an opportunity to substantiate evidence. We may also discover a relationship based on knowledge of surrounding families. Our case though must be clear. We must know the demographics of her neighbors. We must examine the frequencies and breadth of the mtDNA in the area. Knowing this we may calculate for the odds of two people randomly matching each other.

The second goal is to learn the deep ethnic history of our most distant of maternal grandmothers. We as Hs, are all descended from a woman who came to Eurasia from Africa. In the coming years we hope to learn more about the particular path each of her daughters, granddaughters and great-great-great-granddaughters took. To learn this we are studying the geographic origins of each subclade and the haplotypes within the subclades.

To answer either question we must be sure that we understand the tree of descent that connects us. As much as a misattributed marriage record may confuse us as genealogists, so too does a false branch in the phylogenetic tree. Here I will look at what we know at the beginning of the mtDNA Haplogroup Project's third year and where we are going.

Status

The H Haplogroup Project is now at over 2300 members. Haplotype information was assessed at 2348 members for numbers and frequencies of unique haplotypes.

Geography:

Geographic information was extracted from the database at 2348 members.

Origin x Percent
Algeria 1 0.04
Armenia 1 0.04
Austria 12 0.51
Austria-Hungary 8 0.34
Azerbaijan 1 0.04
Azores 7 0.30
Belarus 9 0.38
Belgium 5 0.21
Bohemia 9 0.38
Bosnia 1 0.04
British Isles 718 30.58
Bulgaria 1 0.04
Canary Islands 2 0.09
Croatia 8 0.34
Cyprus 2 0.09
Czech Republic 7 0.30
Czechoslovakia 3 0.13
Denmark 21 0.89
Finland 52 2.21
France 57 2.43
Galicia 1 0.04
Germany 221 9.41
Greece 8 0.34
Holland 9 0.38
Hungary 20 0.85
Iceland 2 0.09
India 3 0.13
Iran 3 0.13
Israel 2 0.09
Italy 62 2.64
Latvia 5 0.21
Lebanon 2 0.09
Lithuania 21 0.89
Luxemburg 2 0.09
Malta 1 0.04
Moldova 5 0.21
Morocco 1 0.04
Netherlands 29 1.24
Norway 56 2.39
Poland 65 2.77
Portugal 14 0.60
Prussia 7 0.30
Romania 7 0.30
Russia 20 0.85
Serbia 1 0.04
Sicily 12 0.51
Slovakia 10 0.43
Slovenia 1 0.04
Spain 28 1.19
Sweden 49 2.09
Switzerland 15 0.64
Turkey 5 0.21
Ukraine 27 1.15
Yugoslavia 2 0.09
Unknown Origin 707 30.11
Total 2348 100.00

Origin x Percent
British Isles 203 28.27
England 234 32.59
Ireland 166 23.12
Isle of Man 1 0.14
Northern Ireland 7 0.97
Scotland 82 11.42
Wales 25 3.48
Total 718 100.00

The most dramatic change to participant origins has been the drop in percentage from the British Isles, 42.78% to 30.58%.

SNPs:

A Single Nucleotide Polymorphism or SNP is a change to a single point in the mtDNA's code. Control region SNPs do not usually by themselves point to a single clade, subclade, or ethnic origin.  Combinations of SNPs form haplotypes that point to a common ancestress.

A total of 154 HVR1 mutations have been found while 195 participants match CRS at HVR1.

037G 111G 146G 172C 184T 213A 223T 243C 262T 283G 293C 304C 324C 354T 398A 524C
038G 111T 147T 174T 185T 214T 224C 245T 263C 284G 293G 309G 325C 355T 399G 525G
042A 114T 148T 176T 188T 215G 234T 248T 265G 286T 294.1A 311C 327A 356C 400T 526A
051G 124C 150T 177G 189C 216G 235G 249C 266T 287T 294G 311G 327T 357C 422C 527T
066G 126C 153A 179T 192A 217C 239A 254G 267T 288C 294T 312G 335G 360T 445C
067T 129A 154C 180G 192T 218T 239G 256T 269G 289G 295T 316G 342C 362C 465T
080G 134T 162G 182C 193T 219G 239T 258G 270T 290G 298C 318G 343G 366T 468C
092C 136C 167T 183C 195C 220G 240G 259T 272G 290T 299G 318T 344T 368C 482G
093C 140C 168T 183G 209C 221T 241G 260T 274A 291T 300G 319A 346C 390A 497G
111A 145A 170G 184A 212G 222T 242T 261T 278T 292T 302G 320T 352C 391A 519C

A total of 126 HVR2 mutations have been found.

010C 058C 073G 153G 198T 227G 256T 292C 327T 417A 485C 522- 533G
016T 060.1T 093G 182T 199C 228A 257G 293C 335G 444G 493G 523- 537T
041T 061T 095C 183G 200G 234G 262T 295A 337- 453C 498- 524.1A 545A
042.1G 063C 114T 185A 204C 235G 263G 309.1C 340T 455.1T 499A 524.1C 553T
044.1C 064T 131C 186A 205A 236C 264T 309.2C 373G 456T 502T 524.2A 573.1C
046C 065C 143A 186T 207A 239C 267C 309.3C 380A 459- 503G 524.2C 573.2C
055C 066A 146C 189G 210G 242T 281G 310C 385G 466C 512C 524.3A
056.1C 071A 150T 194T 214G 246G 288G 315.1C 391C 470G 513A 524.3C
057C 072C 151T 195C 217C 249- 291.1A 315.2C 396T 471C 520T 524.4A
057G 072G 152C 196C 224C 251A 292.1A 316A 408A 477C 521G 524.4C

Haplotypes:

There are now 337 unique HVR1 haplotypes. The twenty most frequent ones are:

HVR1 x
172C,304C,311C 17
189C,356C,519C 17
239T,519C 17
261T,519C 25
311C 25
129A,316G,519C 27
293G,311C 27
093C,519C 30
354T 30
162G,519C 31
189C,356C,362C,519C 33
162G,209C,519C 35
263C,519C 37
129A,519C 42
311C,519C 56
189C,519C 63
362C,482G 81
304C 114
CRS 195
519C 711

210, 62.31%, of the haplotypes are singletons.

There are 318 unique HVR2 haplotypes. The twenty most frequent ones are:

HVR2 x
263G,309.1C,315.1C,477C 8
263G,309.1C,315.1C,522-,523- 8
73G,263G,309.1C,315.1C,522-,523- 8
73G,263G,315.1C,522-,523- 10
146C,263G,309.1C,315.1C 12
93G,263G,315.1C 12
195C,263G,309.1C,315.1C 13
239C,263G,309.1C,309.2C,315.1C 13
239C,263G,309.1C,315.1C 13
263G,315.1C,456T,522-,523- 14
152C,263G,309.1C,315.1C 20
263G,315.1C,522-,523- 21
152C,263G,309.1C,309.2C,315.1C 27
263G,315.1C,477C 28
73G,263G,309.1C,315.1C 31
152C,263G,315.1C 32
73G,263G,315.1C 36
263G,309.1C,309.2C,315.1C 62
263G,309.1C,315.1C 138
263G,315.1C 165

218 out of 318, 68.55%, of the haplotypes are singletons.

Terminology

Maternal Inheritance:

Unlike the majority of our DNA, mtDNA is a separate entity. Once independent, it contains its own DNA and is passed on to us solely from our mothers.

SNPs:

A Single Nucleotide Polymorphism or SNP is a change to a single point in the mtDNA's code.

Subclades:

As papers have tested FGSs for H its subclades have been revised and expanded. Below are some of the published trees for H.

Finnila 2001

  • H
    • H1
    • H2

Herrnstadt 2002

  • H
    • H1
    • H2
    • H3

Loogvali 2004

  • H
    • H1
      • H1a
      • H1b
      • H1f
    • H2
      • H2a
        • H2a
      • H2b
    • H3
    • H4
      • H4a
    • H5
      • H5a
        • H5a1
    • H6
      • H6a
        • H6a1
      • H6b
    • H7
    • H8
    • H9
    • H10
    • H11
      • H11a

Achilli 2004

  • H
    • H1
      • H1a
      • H1b
    • H2
    • H3
      • H3a
    • H4
    • H5
      • H5a
    • H6
      • H6a
      • H6b
    • H7
    • H8
    • H9
    • H10
    • H11
    • H12
    • H13
      • H13a
    • H14
    • H15

Brandstatter 2006

  • H
    • H1
      • H1a
        • H1a1
      • H1b
      • H1c
        • H1c1
        • H1c2
      • H1f
      • H1-8602
      • H1-8473
    • H2
      • H2a
      • H2b
    • H3
      • H3a
      • H3b
      • H3c
    • H4
      • H4a
        • H4a1
    • H5
      • H5a
        • H5a1
    • H6
      • H6a
        • H6a1
    • H7
    • H8
    • H9
    • H10
    • H11
    • H12
    • H13
      • H13a
        • H13a1
    • H14
    • H15
    • H16
    • H17
    • H-709

Roostalu 2007

  • H
    • H1
      • H1a
        • H1a1
        • H1a2
      • H1b
      • H1c
        • H1c1
        • H1c2
      • H1d
      • H1f
    • H2
      • H2a
        • H2a1
        • H2a2
      • H2b
    • H3
      • H3a
      • H3b
      • H3c
    • H4
      • H4a
        • H4a1
          • H4a1a
      • H4b
    • H5
      • H5a
        • H5a1
    • H6
      • H6a
        • H6a1
      • H6b
    • H7
    • H8
    • H9
    • H10
    • H11
      • H11a
    • H12
    • H13
      • H13a
        • H13a1
        • H13a2
    • H14
      • H14a
    • H15
    • H16
    • H17
    • H18
    • H19
    • H20
    • H21

Math:

There are two calculations that are done for each data set. They are calculated with several variables. The number of people in the sample is called n. The number of unique haplotypes is called m. The number of people with any one haplotype is called x.

The Random Matching Probability, RMP, measures the probability of picking two matching haplotypes out of a population and having them be unrelated. A lower RMP means that a chance match is less likely. Then if two people are found to have been neighbors and the RMP is sufficiently low a family relationship can be inferred. To find the RMP each x is first squared, the sum of these squares is multiplied by one over n squared.

Here is an example:

Haplotype x x^2
Hap1 5 25
Hap2 3 9
Hap3 1 1
Hap4 7 49
Sum of x^2—> 84

n is 5+3+1+7 or 16. 16 squared is 256. So 1/256 is multiplied by 84. This gives us .328125. Multiplying by 100 changes the answer to a percentage, 32.8125%.

Diversity is a simple measure of how many different haplotypes there are in a sample in proportion to the size of the sample. Here it is a higher diversity that indicates a lower probability of a chance match. It is found by dividing m by n. Looking at the above sample, m is 4 because there are 4 unique haplotypes. 4 is then divided by n, 16, for .25. Multiplying by 100 changes the answer to a percentage, 25%.

Haplotype Analysis:

In any sample of H haplotypes there will be some that are identical to each other and some that only occur once. Five HVR1 haplotypes picked at random from a population might be:

16519C
16519C
16051G,16162G,16259T,16519C
16051G,16162G,16259T,16519C
16126C,16519C

To better organize these results they can be sorted into unique haplotypes with frequencies.

16051G,16162G,16259T,16519C 2
16126C,16519C 1
16519C 2

This makes the math that was mentioned above much easier to perform.

Match Probability Analysis

HVR1:

There are 337 unique haplotypes in a sample of 2348. This is a ratio of 337 to 2348 or a diversity of 14.35%. The Random Match probability is 10.64%. The combination of a low diversity and a higher random match probability indicates that HVR1 by itself is a poor method to distinguish H lineages. It should also be noted that at n =796 the HVR1 diversity was 19.47% while the random match probability was 12.01%.

HVR1 (1600+) x x^2
037G 1 1
038G,092C,214T,519C 1 1
042A,243C,519C 1 1
051G,129A,162G,465T,519C 1 1
051G,162G,185T,519C,527T 1 1
051G,162G,259T,519C 2 4
051G,162G,266T,519C 6 36
051G,162G,343G,519C 2 4
051G,162G,465T,519C 11 121
051G,162G,519C 15 225
051G,311C,356C,519C 1 1
051G,519C 1 1
066G,519C 2 4
067T,172C,240G,261T 1 1
067T,183C,189C,519C 14 196
067T,311C 1 1
067T,355T,519C 1 1
080G,189C,223T,356C,519C 1 1
080G,189C,356C 1 1
092C,129A,239T,519C 1 1
092C,140C,311C 4 16
092C,140C,311C,526A 1 1
092C,183C,189C,519C 1 1
092C,293G,311C 1 1
092C,298C,311C 1 1
092C,519C 3 9
093C 4 16
093C,124C,221T,519C 1 1
093C,129A,278T,316G,519C 1 1
093C,129A,316G,519C 2 4
093C,129A,519C 4 16
093C,168T,519C 1 1
093C,183C,189C,278T,519C 1 1
093C,189C,356C,362C,519C 1 1
093C,189C,368C,519C 1 1
093C,221T,316G,519C 1 1
093C,221T,519C 13 169
093C,265G,519C 2 4
093C,291T,519C 1 1
093C,300G,519C 1 1
093C,304C 1 1
093C,311C,519C 5 25
093C,362C,482G 2 4
093C,519C 30 900
093C,519C,527T 1 1
111A,519C 7 49
111G,519C 1 1
111T,129A,256T,311C,519C 1 1
111T,129A,256T,519C 9 81
111T,167T,288C,362C,519C 1 1
111T,293G,311C 2 4
111T,295T,519C 1 1
111T,519C 1 1
114T,126C,519C 2 4
114T,189C,356C,519C 1 1
114T,344T,519C 4 16
114T,519C 16 256
124C,354T 1 1
126C 1 1
126C,223T,260T,298C 2 4
126C,261T,519C 1 1
126C,298C,346C 1 1
126C,519C 2 4
129A 13 169
129A,147T,316G,519C 1 1
129A,162G,209C,519C 1 1
129A,162G,519C 1 1
129A,184T 1 1
129A,189C,355T,356C,362C,519C 4 16
129A,189C,519C 1 1
129A,239T,519C 1 1
129A,249C,362C,482G 2 4
129A,249C,519C 1 1
129A,293G,316G,335G,519C 1 1
129A,298C 2 4
129A,300G,519C 1 1
129A,304C 3 9
129A,316G,519C 27 729
129A,354T 1 1
129A,357C,519C 1 1
129A,519C 42 1764
134T,292T,362C,482G 1 1
134T,362C,482G 2 4
136C,295T,519C 1 1
136C,519C 2 4
140C,189C,293G,311C 1 1
140C,265G,293G,311C 2 4
140C,287T,519C 1 1
140C,293G,311C 4 16
145A 1 1
145A,274A,343G,519C 1 1
145A,519C 5 25
146G,519C 1 1
147T,519C 1 1
148T,261T,519C 1 1
148T,519C 14 196
150T,519C 1 1
153A 1 1
153A,288C,362C 2 4
153A,519C 1 1
154C,362C,482G 1 1
162G,174T,209C,519C 1 1
162G,189C,294.1A,519C 1 1
162G,209C,295T,519C 1 1
162G,209C,519C 35 1225
162G,290G,519C 1 1
162G,362C,519C 1 1
162G,519C 31 961
167T,519C 1 1
168T,519C 7 49
170G,256T,295T,519C 1 1
170G,256T,309G,519C 1 1
170G,256T,519C 1 1
172C 1 1
172C,183C,189C,356C,362C,519C 2 4
172C,209C,519C 1 1
172C,217C 1 1
172C,304C 1 1
172C,304C,311C 17 289
172C,311C 1 1
172C,362C,519C 4 16
172C,519C 12 144
172C,519C,527T 1 1
174T,311C,519C 1 1
176T 1 1
176T,354T 1 1
177G,519C 3 9
179T 1 1
179T,183C,189C,519C 1 1
180G,311C 1 1
182C,183C,189C,356C,519C 1 1
182C,183C,189C,362C,519C 2 4
183C,189C,192A,519C 1 1
183C,189C,239T,519C 1 1
183C,189C,256T,352C 1 1
183C,189C,261T,519C 1 1
183C,189C,274A,519C 1 1
183C,189C,356C,362C,519C 5 25
183C,189C,356C,519C 14 196
183C,189C,356C,519C,527T 2 4
183C,189C,362C,519C 1 1
183C,189C,519C 7 49
183G,390A,519C 1 1
184A,320T,368C,519C 1 1
184T 1 1
184T,189C,519C 1 1
184T,304C 1 1
184T,362C,400T,482G 1 1
184T,519C 3 9
185T,519C 1 1
188T 1 1
188T,304C 1 1
188T,311C,519C 1 1
188T,519C 2 4
189C 2 4
189C,260T,519C 1 1
189C,278T,519C 1 1
189C,290T,291T,356C,362C,519C 1 1
189C,290T,519C 2 4
189C,291T,304C 1 1
189C,298C,357C 1 1
189C,298C,519C 1 1
189C,299G,422C,519C 2 4
189C,300G,362C,482G 1 1
189C,304C 1 1
189C,304C,519C 1 1
189C,311C 1 1
189C,316G,519C 1 1
189C,356C 1 1
189C,356C,362C,519C 33 1089
189C,356C,519C 17 289
189C,362C,519C 1 1
189C,519C 63 3969
192T,304C 2 4
192T,304C,335G 1 1
192T,362C,445C,482G 1 1
192T,519C 1 1
193T,219G,362C,482G 2 4
193T,239T,519C 1 1
193T,519C 6 36
195C 2 4
195C,291T,519C 1 1
209C 1 1
209C,304C,519C 1 1
209C,519C 10 100
212G 1 1
213A,216G,304C 1 1
215G,266T,519C 1 1
215G,354T 2 4
217C,218T,242T,519C 1 1
218T,519C 2 4
220G,519C 2 4
221T,290T,294T,519C 1 1
221T,519C 13 169
222T,299G,519C 1 1
223T,362C,482G 1 1
223T,519C 1 1
224C,288C,362C,519C 1 1
224C,398A,519C 1 1
234T,293G,519C 1 1
234T,519C 3 9
235G,239T,291T,293G,311C,400T 1 1
235G,290T,291T 1 1
235G,291T 12 144
235G,291T,293G 1 1
235G,291T,293G,400T 3 9
235G,293G,400T 1 1
239A,519C 1 1
239G,256T,311C,519C 1 1
239G,290T,519C 1 1
239G,519C 9 81
239T,286T,519C 1 1
239T,519C 17 289
240G,309G,519C 1 1
240G,519C 1 1
241G,287T,519C 1 1
242T,362C 1 1
243C,293G,311C 1 1
243C,304C 1 1
243C,519C 1 1
245T,519C 1 1
248T,298C 1 1
248T,318T,519C 1 1
248T,519C 5 25
249C,362C,482G 9 81
254G,311C,519C 1 1
254G,356C,519C 1 1
256T 1 1
256T,272G,352C 1 1
256T,293G,311C,525G 1 1
256T,352C 1 1
256T,354T 3 9
256T,519C 9 81
258G,319A,320T,519C 1 1
259T,311C,519C 1 1
259T,519C 3 9
260T 2 4
260T,519C 3 9
261T 1 1
261T,298C 1 1
261T,304C,519C 1 1
261T,311C 2 4
261T,519C 25 625
262T,278T,519C 1 1
263C,519C 37 1369
265G,311C 1 1
265G,519C 1 1
266T 1 1
267T,519C 1 1
269G 1 1
269G,298C 1 1
270T 1 1
270T,519C 1 1
274A,294G,519C 1 1
274A,519C 2 4
278T,293G,311C 8 64
278T,304C,311C 1 1
278T,311C,519C 1 1
278T,519C 5 25
283G,304C 1 1
284G,294T,304C 1 1
284G,519C 3 9
286T,311C 2 4
286T,519C 1 1
287T 3 9
288C,362C 11 121
289G,519C 2 4
291T 1 1
291T,293G 1 1
291T,304C 1 1
291T,390A,519C 1 1
291T,519C 9 81
293C,519C 2 4
293G,311C 27 729
293G,311C,368C 3 9
293G,519C 5 25
294T,304C 1 1
294T,362C,482G 1 1
298C 10 100
298C,311C 2 4
298C,324C 1 1
298C,354T,390A,519C 1 1
299G,311C 1 1
299G,519C 12 144
300G,344T,519C 1 1
300G,362C 1 1
302G,304C 1 1
302G,468C,519C 3 9
302G,519C 1 1
304C 114 12996
304C,311C 1 1
304C,311C,362C 2 4
304C,311C,391A 1 1
304C,343G 1 1
304C,357C 2 4
304C,362C 1 1
304C,390A 1 1
304C,519C 12 144
311C 25 625
311C,354T,519C 1 1
311C,355T,519C 1 1
311C,357C,519C 2 4
311C,360T,519C 1 1
311C,390A 1 1
311C,497G,519C 1 1
311C,519C 56 3136
311G,519C 1 1
312G,519C 2 4
318G,519C 1 1
318T,519C 1 1
319A,519C 7 49
325C,362C 1 1
325C,519C 6 36
327A 1 1
327T,519C 4 16
342C,519C 2 4
354T 30 900
354T,519C 4 16
355T,519C 4 16
356C 1 1
357C,519C 2 4
362C,482G 81 6561
362C,482G,519C 1 1
362C,519C 15 225
366T 2 4
368C,519C 1 1
390A,519C 3 9
399G 1 1
399G,519C 5 25
465T,519C 1 1
468C,519C 2 4
519C 711 505521
519C,524C 1 1
519C,527T 4 16
526A 1 1
CRS 195 38025

HVR2:

There are 318 unique haplotypes in a sample of 1155. This is a ratio of 318 to 1155 or 27.53%. The random match probability is 4.38%. Although this is an improvement when compared to the HVR1 results, it is still not a genealogically useful determinant. At n=368 the HVR2 diversity was 40.22% while the random match probability was 4.71%.

HVR2 x x^2
10C,263G,315.1C 1 1
114T,146C,152C,195C,263G,315.1C 1 1
131C,152C,207A,263G,309.1C,315.1C 1 1
131C,152C,263G,309.1C,315.1C 1 1
131C,195C,263G,309.1C,315.1C 1 1
131C,263G,315.1C 1 1
131C,263G,456T 1 1
146C,152C,195C,263G,309.1C,315.1C 1 1
146C,152C,195C,263G,315.1C 1 1
146C,152C,207A,263G,315.1C,522-,523- 2 4
146C,152C,239C,263G,309.1C,315.1C 1 1
146C,152C,263G,309.1C,309.2C,315.1C 1 1
146C,152C,263G,309.1C,315.1C 2 4
146C,152C,263G,315.1C 1 1
146C,153G,263G,309.1C,315.1C,524.1C,524.2A 1 1
146C,195C,263G,309.1C,309.2C,315.1C,456T 1 1
146C,195C,263G,309.1C,309.2C,315.1C,522-,523- 1 1
146C,195C,263G,309.1C,315.1C 2 4
146C,195C,263G,309.1C,315.1C,456T 3 9
146C,195C,263G,315.1C 5 25
146C,195C,263G,315.1C,471C 2 4
146C,195C,263G,315.1C,522-,523- 1 1
146C,217C,263G,315.1C 1 1
146C,239C,263G,309.1C,309.2C,315.1C 1 1
146C,239C,263G,309.1C,309.2C,315.1C,553T 1 1
146C,263G,309.1C,309.2C,315.1C 4 16
146C,263G,309.1C,309.2C,315.1C,453C 1 1
146C,263G,309.1C,309.2C,315.1C,456T 1 1
146C,263G,309.1C,309.2C,315.1C,456T,573.1C,573.2C 1 1
146C,263G,309.1C,309.2C,315.1C,524.1C,524.2A 2 4
146C,263G,309.1C,309.2C,315.1C,524.1C,524.2A,573.1C 1 1
146C,263G,309.1C,315.1C 12 144
146C,263G,309.1C,315.1C,456T 2 4
146C,263G,309.1C,315.1C,493G 1 1
146C,263G,315.1C 5 25
146C,263G,315.1C,456T,573.1C,573.2C 1 1
150T,152C,263G,315.1C 1 1
150T,195C,263G,309.1C,309.2C,315.1C 1 1
150T,195C,263G,309.1C,309.2C,315.1C,522-,523- 1 1
150T,263G,309.1C,309.2C,315.1C 3 9
150T,263G,309.1C,309.2C,315.1C,456T,522-,523- 1 1
150T,263G,309.1C,315.1C 4 16
150T,263G,309.1C,315.1C,456T 1 1
150T,263G,310C 1 1
150T,263G,315.1C 2 4
150T,263G,315.1C,456T 1 1
151T,152C,263G,309.1C,315.1C 1 1
151T,152C,263G,315.1C 3 9
151T,195C,263G,309.1C,309.2C,315.1C 2 4
151T,263G,291.1A,315.1C 1 1
151T,263G,309.1C,309.2C,315.1C 1 1
151T,263G,309.1C,315.1C,477C 1 1
151T,263G,315.1C 1 1
152C,153G,204C,263G,309.1C,309.2C,315.1C 1 1
152C,183G,263G,309.1C,315.1C 1 1
152C,194T,263G,315.1C 1 1
152C,194T,263G,315.1C,522-,523- 1 1
152C,195C,198T,263G,309.1C,309.2C,315.1C 1 1
152C,195C,263G,309.1C,309.2C,315.1C 2 4
152C,195C,263G,309.1C,315.1C 2 4
152C,195C,263G,309.1C,315.1C,513A 1 1
152C,195C,263G,309.1C,315.1C,522-,523- 1 1
152C,195C,263G,315.1C 3 9
152C,199C,263G,315.1C,524.1A,524.2C 1 1
152C,199C,263G,315.1C,524.1C,524.2A 1 1
152C,200G,263G,309.1C,309.2C,315.1C 1 1
152C,200G,263G,309.1C,309.2C,315.1C,444G,456T,522-,523- 2 4
152C,200G,263G,309.1C,315.1C 1 1
152C,200G,263G,315.1C 1 1
152C,200G,263G,315.1C,444G,456T,522-,523- 1 1
152C,228A,263G,309.1C,315.1C 1 1
152C,239C,263G,309.1C,309.2C,315.1C 2 4
152C,239C,263G,309.1C,315.1C 2 4
152C,239C,263G,315.1C 1 1
152C,263G,293C,309.1C,309.2C,315.1C 2 4
152C,263G,293C,309.1C,315.1C 1 1
152C,263G,309.1C,309.2C,315.1C 27 729
152C,263G,309.1C,309.2C,315.1C,456T,513A 1 1
152C,263G,309.1C,309.2C,315.1C,456T,522-,523- 1 1
152C,263G,309.1C,309.2C,315.1C,477C 1 1
152C,263G,309.1C,309.2C,315.1C,524.1C,524.2A 2 4
152C,263G,309.1C,315.1C 20 400
152C,263G,309.1C,315.1C,316A 1 1
152C,263G,309.1C,315.1C,456T,513A 1 1
152C,263G,309.1C,315.1C,456T,522-,523- 2 4
152C,263G,309.1C,315.1C,477C 1 1
152C,263G,309.1C,315.1C,522-,523- 3 9
152C,263G,309.1C,315.1C,524.1C,524.2A 1 1
152C,263G,309.1C,315.1C,537T 2 4
152C,263G,309.1C,315.1C,573.1C,573.2C 1 1
152C,263G,315.1C 32 1024
152C,263G,315.1C,340T,456T 1 1
152C,263G,315.1C,444G,456T,522-,523- 4 16
152C,263G,315.1C,455.1T 1 1
152C,263G,315.1C,456T 1 1
152C,263G,315.1C,456T,522-,523- 4 16
152C,263G,315.1C,477C 3 9
152C,263G,315.1C,522-,523- 3 9
152C,263G,315.1C,524.1C,524.2A 8 64
152C,309.1C,309.2C,315.1C 3 9
153G,199C,204C,263G,309.1C,309.2C,315.1C 1 1
153G,263G,309.1C,309.2C,315.1C 2 4
153G,263G,309.1C,315.1C 1 1
16T,146C,239C,263G,309.1C,315.1C 1 1
182T,263G,315.1C 1 1
183G,263G,309.1C,309.2C,315.1C 2 4
183G,263G,309.1C,315.1C 1 1
183G,315.1C 1 1
185A,195C,263G,309.1C,309.2C,315.1C 1 1
185A,263G,309.1C,315.1C,513A 1 1
186A,263G,309.1C,315.1C 2 4
186A,263G,315.1C 3 9
186T,263G,315.1C,456T,522-,523- 1 1
189G,263G,309.1C,309.2C,315.1C 1 1
189G,263G,309.1C,315.1C 1 1
189G,263G,315.1C 1 1
189G,309.1C,315.1C 1 1
194T,205A,263G,309.1C,309.2C,315.1C,522-,523-,573.1C 1 1
194T,263G,315.1C 1 1
195C,228A,263G,309.1C,309.2C,315.1C 1 1
195C,239C,263G,309.1C,309.2C,315.1C 2 4
195C,239C,263G,315.1C 1 1
195C,257G,263G,309.1C,309.2C,315.1C,477C 3 9
195C,257G,263G,309.1C,315.1C 1 1
195C,257G,263G,309.1C,315.1C,477C 5 25
195C,263G,292C,315.1C 1 1
195C,263G,309.1C,309.2C,315.1C 4 16
195C,263G,309.1C,315.1C 13 169
195C,263G,309.1C,315.1C,513A 1 1
195C,263G,309.1C,315.1C,524.1C,524.2A 1 1
195C,263G,315.1C 8 64
195C,263G,315.1C,335G 3 9
195C,263G,315.1C,477C 1 1
195C,263G,315.1C,477C,513A 1 1
195C,263G,315.1C,513A,522-,523- 1 1
195C,263G,315.1C,522-,523- 7 49
195C,263G,315.1C,522-,523-,573.1C,573.2C 1 1
195C,263G,315.1C,524.1C,524.2A 1 1
196C,263G,309.1C,309.2C,315.1C 1 1
199C,236C,263G,309.1C,309.2C,315.1C 1 1
199C,263G,309.1C,309.2C,315.1C 1 1
199C,263G,309.1C,315.1C 1 1
199C,263G,309.1C,315.1C,456T,513A 1 1
199C,263G,315.1C 3 9
200G,227G,263G,309.1C,315.1C 1 1
200G,263G,309.1C,309.2C,315.1C 1 1
200G,263G,309.1C,309.2C,315.1C,524.1C,524.2A 1 1
200G,263G,309.1C,315.1C 3 9
200G,263G,315.1C 1 1
200G,263G,315.1C,522-,523- 1 1
204C,239C,263G,309.1C,309.2C,315.1C,524.1C,524.2A 1 1
204C,239C,263G,309.1C,315.1C 1 1
204C,263G,309.1C,309.2C,315.1C 1 1
204C,263G,315.1C 1 1
204C,315.1C 1 1
207A,239C,263G,309.1C,315.1C 1 1
210G,263G,309.1C,309.2C,315.1C 2 4
214G,263G,315.1C,522-,523- 1 1
224C,263G,309.1C,309.2C,315.1C,499A 1 1
234G,263G,309.1C,315.1C,477C 1 1
234G,263G,315.1C 1 1
235G,263G,315.1C 1 1
236C,263G,309.1C,315.1C 1 1
239C,263G,288G,309.1C,315.1C 1 1
239C,263G,309.1C,309.2C,315.1C 13 169
239C,263G,309.1C,309.2C,315.1C,524.1C,524.2A 2 4
239C,263G,309.1C,309.2C,315.1C,573.1C,573.2C 1 1
239C,263G,309.1C,315.1C 13 169
239C,263G,309.1C,315.1C,466C 1 1
239C,263G,315.1C 8 64
242T,263G,309.1C,315.1C,408A 1 1
246G,263G,309.1C,315.1C 1 1
249-,263G,309.1C,315.1C 1 1
251A,263G,315.1C 1 1
256T,263G,315.1C 2 4
257G,263G,309.1C,309.2C,315.1C,477C 3 9
257G,263G,315.1C,477C 4 16
262T,263G,309.1C,315.1C 1 1
263G,264T,315.1C 1 1
263G,267C,309.1C,309.2C,315.1C,485C 1 1
263G,291.1A,309.1C,315.1C 1 1
263G,291.1A,315.1C 1 1
263G,292.1A,315.1C 1 1
263G,293C,309.1C,309.2C,315.1C 1 1
263G,293C,315.1C 3 9
263G,309.1C,309.2C 1 1
263G,309.1C,309.2C,315.1C 62 3844
263G,309.1C,309.2C,315.1C,327T,456T 3 9
263G,309.1C,309.2C,315.1C,385G 1 1
263G,309.1C,309.2C,315.1C,408A 1 1
263G,309.1C,309.2C,315.1C,417A 1 1
263G,309.1C,309.2C,315.1C,456T 6 36
263G,309.1C,309.2C,315.1C,456T,522-,523- 2 4
263G,309.1C,309.2C,315.1C,456T,524.1C,524.2A 1 1
263G,309.1C,309.2C,315.1C,477C 4 16
263G,309.1C,309.2C,315.1C,477C,522-,523- 1 1
263G,309.1C,309.2C,315.1C,522-,523- 8 64
263G,309.1C,309.2C,315.1C,522-,523-,533G 1 1
263G,309.1C,309.2C,315.1C,524.1C,524.1A 1 1
263G,309.1C,309.2C,315.1C,524.1C,524.2A 6 36
263G,309.1C,309.2C,456T,522-,523- 1 1
263G,309.1C,315.1C 138 19044
263G,309.1C,315.1C,316A 1 1
263G,309.1C,315.1C,337-,456T,522-,523- 1 1
263G,309.1C,315.1C,391C 1 1
263G,309.1C,315.1C,408A 3 9
263G,309.1C,315.1C,456T 6 36
263G,309.1C,315.1C,456T,522-,523- 4 16
263G,309.1C,315.1C,477C 8 64
263G,309.1C,315.1C,477C,513A 1 1
263G,309.1C,315.1C,477C,524.1C,524.2A 2 4
263G,309.1C,315.1C,499A,524.1C,524.2A 1 1
263G,309.1C,315.1C,502T 1 1
263G,309.1C,315.1C,512C 1 1
263G,309.1C,315.1C,513A 4 16
263G,309.1C,315.1C,522-,523- 8 64
263G,309.1C,315.1C,573.1C,573.2C 1 1
263G,315.1C 165 27225
263G,315.1C,315.2C 1 1
263G,315.1C,380A 1 1
263G,315.1C,408A 3 9
263G,315.1C,444G,456T,522-,523- 7 49
263G,315.1C,456T 7 49
263G,315.1C,456T,522-,523- 14 196
263G,315.1C,456T,524.1A,524.2C,524.3A,524.4C 1 1
263G,315.1C,456T,524.1C,524.2A,524.3C,524.4A 1 1
263G,315.1C,459- 1 1
263G,315.1C,466C 1 1
263G,315.1C,477C 28 784
263G,315.1C,477C,522-,523- 1 1
263G,315.1C,503G 1 1
263G,315.1C,520T,573.1C 1 1
263G,315.1C,521G 2 4
263G,315.1C,522-,523- 21 441
263G,315.1C,524.1C,524.2A 4 16
263G,315.1C,524.1C,524.2A,524.3C,524.4A 1 1
309.1C,309.2C,315.1C 4 16
309.1C,309.2C,315.1C,327T,456T 1 1
309.1C,315.1C 3 9
315.1C 6 36
41T,263G,309.1C,315.1C,477C 1 1
42.1G,195C,263G,309.1C,309.2C,315.1C 1 1
44.1C,152C,214G,239C,263G,309.1C,309.2C,315.1C,533G 1 1
44.1C,239C,263G,309.1C,309.2C,315.1C 1 1
44.1C,263G,309.1C,309.2C,315.1C 1 1
44.1C,55C,57C,146C,263G,309.1C,315.1C 1 1
46C,263G,315.1C,477C 1 1
55C,56.1C,263G,309.1C,315.1C 1 1
55C,57C,263G,309.1C,309.2C,315.1C 1 1
55C,57C,61T,263G,309.1C,315.1C 1 1
55C,57G,263G,309.1C,309.2C,315.1C 1 1
55C,57G,263G,309.1C,315.1C 1 1
56.1C,58C,73G,195C,263G,309.1C,315.1C 1 1
60.1T,71A,153G,204C,207A,263G,309.1C,309.2C,309.3C,315.1C,373G 1 1
63C,64T,66A,239C,263G,315.1C 1 1
64T,195C,263G,309.1C,309.2C,315.1C,522-,523- 1 1
64T,263G,315.1C 1 1
64T,65C,152C,263G,315.1C 1 1
72C,152C,195C,263G,315.1C 1 1
72C,152C,263G,315.1C 1 1
72C,195C,198T,263G,309.1C,315.1C 1 1
72C,195C,263G,309.1C,315.1C 2 4
72C,195C,263G,315.1C 1 1
72C,195C,263G,315.1C,524.1C,524.2A 1 1
72C,200G,263G,315.1C 1 1
72C,200G,263G,315.1C,522-,523- 1 1
72C,263G,309.1C,315.1C 2 4
72C,263G,315.1C 1 1
72C,93G,195C,263G,309.1C,315.1C 1 1
72G,146C,195C,263G,309.1C,309.2C,315.1C 1 1
72G,146C,195C,263G,309.1C,315.1C 2 4
72G,263G,309.1C,315.1C 2 4
73G,143A,146C,263G,309.1C,315.1C 1 1
73G,143A,146C,263G,309.1C,315.1C,385G 1 1
73G,143A,146C,263G,315.1C 1 1
73G,146C,152C,263G,315.1C,498- 1 1
73G,146C,263G,309.1C,315.1C,522-,523- 1 1
73G,146C,263G,315.1C,522-,523- 2 4
73G,150T,263G,309.1C,309.2C,315.1C 1 1
73G,151T,263G,315.1C 1 1
73G,152C,263G,309.1C,315.1C 1 1
73G,152C,263G,309.1C,315.1C,522-,523- 1 1
73G,152C,263G,315.1C 1 1
73G,189G,263G,295A,309.1C,315.1C,522-,523- 1 1
73G,195C,263G,309.1C,315.1C 1 1
73G,195C,263G,315.1C,522-,523- 1 1
73G,204C,263G,309.1C,315.1C,522-,523- 2 4
73G,228A,263G,315.1C 1 1
73G,239C,263G,309.1C,315.1C 1 1
73G,263G,281G,315.1C,408A 1 1
73G,263G,309.1C,309.2C,315.1C 1 1
73G,263G,309.1C,315.1C 31 961
73G,263G,309.1C,315.1C,522-,523- 8 64
73G,263G,309.1C,315.1C,545A 1 1
73G,263G,315.1C 36 1296
73G,263G,315.1C,456T,522-,523- 1 1
73G,263G,315.1C,522-,523- 10 100
73G,263G,315.1C,524.1C,524.2A 1 1
73G,263G,315.1C,573.1C,573.2C 2 4
73G,93G,195C,263G,315.1C 1 1
73G,93G,263G,315.1C 1 1
93G,152C,263G,315.1C 1 1
93G,186A,263G,309.1C,315.1C 1 1
93G,200G,263G,315.1C 1 1
93G,263G,309.1C,309.2C,315.1C 2 4
93G,263G,309.1C,315.1C 1 1
93G,263G,309.1C,315.1C,456T,470G,522-,523- 1 1
93G,263G,309.1C,315.1C,522-,523- 1 1
93G,263G,315.1C 12 144
93G,263G,315.1C,513A 1 1
93G,263G,315.1C,522-,523- 1 1
93G,315.1C 1 1
93G,315.1C,524.1C,524.2A 1 1
93G,95C,263G,309.1C,315.1C 1 1
93G,95C,263G,315.1C,522-,523- 1 1
95C,152C,263G,309.1C,315.1C,396T 1 1
95C,195C,263G,309.1C,315.1C 1 1
CRS 3 9

HVR1 and HVR2:

The combination of HVR1 & HVR2 increases diversity. There are 640 combination haplotypes in a sample of 1155. This is a ratio of 640 to 1155 or 55.41% The random match probability is .72%. This is just over the level of diversity we are looking for.  At n=368 the combined HVR1 and HVR2 diversity was 70.11% and the random match probability was 1.02%.

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HVR1 (16000+) HVR2 x x^2
037G 152C,263G,309.1C,315.1C 1 1
038G,092C,214T,519C 263G,315.1C 1 1
042A,243C,519C 73G,263G,309.1C,315.1C 1 1
051G,162G,185T,519C,527T 73G,263G,309.1C,315.1C 1 1
051G,162G,266T,519C 73G,263G,315.1C 3 9
051G,162G,266T,519C 73G,93G,263G,315.1C 1 1
051G,162G,343G,519C 73G,263G,315.1C 1 1
051G,162G,465T,519C 73G,195C,263G,315.1C,522-,523- 1 1
051G,162G,465T,519C 73G,263G,309.1C,315.1C,522-,523- 1 1
051G,162G,465T,519C 73G,263G,315.1C,522-,523- 4 16
051G,162G,519C 56.1C,58C,73G,195C,263G,309.1C,315.1C 1 1
051G,162G,519C 73G,263G,309.1C,315.1C 1 1
051G,162G,519C 73G,263G,315.1C 2 4
051G,162G,519C 73G,263G,315.1C,522-,523- 2 4
051G,162G,519C 73G,93G,195C,263G,315.1C 1 1
051G,311C,356C,519C 131C,195C,263G,309.1C,315.1C 1 1
051G,519C 246G,263G,309.1C,315.1C 1 1
067T,183C,189C,519C 152C,263G,309.1C,309.2C,315.1C 11 121
080G,189C,223T,356C,519C 151T,263G,309.1C,309.2C,315.1C 1 1
080G,189C,356C 73G,263G,315.1C 1 1
092C,129A,239T,519C 73G,263G,315.1C 1 1
092C,140C,311C 195C,263G,309.1C,315.1C 2 4
092C,140C,311C 195C,263G,315.1C 1 1
092C,293G,311C 146C,195C,263G,315.1C 1 1
092C,519C 73G,152C,263G,309.1C,315.1C 1 1
093C 263G,309.1C,315.1C 1 1
093C 263G,315.1C 1 1
093C,129A,278T,316G,519C 263G,315.1C 1 1
093C,129A,316G,519C 263G,315.1C 1 1
093C,129A,519C 263G,309.1C,315.1C 1 1
093C,129A,519C 263G,315.1C 1 1
093C,183C,189C,278T,519C 44.1C,263G,309.1C,309.2C,315.1C 1 1
093C,189C,356C,362C,519C 263G,315.1C,522-,523- 1 1
093C,189C,368C,519C 263G,315.1C 1 1
093C,221T,316G,519C 263G,309.1C,315.1C 1 1
093C,221T,519C 152C,263G,309.1C,309.2C,315.1C 1 1
093C,221T,519C 152C,263G,309.1C,315.1C 1 1
093C,221T,519C 263G,309.1C,309.2C,315.1C 1 1
093C,221T,519C 263G,309.1C,315.1C 8 64
093C,221T,519C 263G,315.1C 1 1
093C,265G,519C 263G,315.1C 1 1
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