Thom

BigY2: IN31134

Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > BY70330

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRBigY2
IN31134
19718337-G-A 17606457-G-A P5_Prx A*
19774707-T-G 17662827-T-G P5_Prx A*
20704653-A-G 18542767-A-G P4_Prx A*
22232655-T-A 20070769-T-A DYZ19 A*
24251854-C-G 22105707-C-G P3_b1 A*
25887275-G-A 23741128-G-A P1_Y1 A*
26095807-T-A 23949660-T-A P1_Y1 A*
7416995-G-C 7548954-G-C BY160548 YY+
8790747-A-G 8922706-A-G BY160286 YY+
9072295-T-C 9234686-T-C BY160241 Y+
9417388-G-A 9579779-G-A BY160208 YY+
9840725-C-T 10003116-C-T YY+
9884869-G-A 10047260-G-A YY+
14590698-C-G 12478898-C-G BY160015 YY+
15270512-T-C 13158601-T-C BY159952 YY+
16361168-G-A 14249288-G-A BY159813 YY+
16517741-G-C 14405861-G-C BY159783 YY+
16583389-A-C 14471509-A-C BY159764 YY+
16584703-C-A 14472823-C-A BY159763 YY+
17457557-C-T 15345677-C-T YY+
17666251-G-T 15554371-G-T BY159566 YY+
17679481-C-T 15567601-C-T BY159564 YY+
17773410-G-A 15661530-G-A BY159541 YY+
17948659-T-G 15836779-T-G BY159507 YY+
18850784-G-A 16738904-G-A BY159359 YY+
19441628-C-T 17329748-C-T BY159240 YY+
19719250-TG-T 17607370-TG-T P5_Prx +
21405389-G-A 19243503-G-A BY159160 YY+
21440320-G-A 19278434-G-A BY159151 YY+
21606823-C-T 19444937-C-T BY159126 YY+
21646482-C-A 19484596-C-A YY+
21758206-A-G 19596320-A-G BY159093 YY+
21995222-C-T 19833336-C-T BY159056 YY+
22229113-G-A 20067227-G-A BY52113 DYZ19 +
22236019-A-G 20074133-A-G BY174711 DYZ19 +
22241889-C-A 20080003-C-A BY214002 DYZ19 +
22441727-A-T 20279841-A-T BY219035 DYZ19 +
22478214-G-C 20316328-G-C FT460091 DYZ19 +
22742383-T-C 20580497-T-C BY158935 YY+
22928304-A-G 20766418-A-G BY158902 YY+
23070612-C-T 20908726-C-T BY158878 YY+
23404232-C-G 21242346-C-G BY158812 YY+
23784695-G-A 21622809-G-A BY158759 Y+
23989732-C-T 21843585-C-T BY158731 Y+
9533796-A-ATG 9696187-A-ATG IR3_Prx 8×TG*
13691967-G-C 11536291-G-C *
22302241-A-T 20140355-A-T DYZ19 *
22318893-T-A 20157007-T-A DYZ19 *
13859448-A-T 11738742-A-T **
13859459-G-T 11738753-G-T **
3324074-CAG-C 3456033-CAG-C **
15157385-C-A 13045472-C-A **
13859385-G-C 11738679-G-C **
20420214-G-T 18258328-G-T P5_Dst **
19012481-C-A 16900601-C-A **
19544401-A-C 17432521-A-C **
13859450-A-G 11738744-A-G **
10827110-A-G **
4395418-C-A 4527377-C-A **
11643673-G-A **
13454414-C-A 11298738-C-A **
10989173-A-C **
56850217-C-A **
10944888-T-G **
10960396-G-C **
27998520-T-A 25852373-T-A P1_Y2 **
14537980-C-A 12426181-C-A **
10976647-T-A **
10887944-C-A **
10888005-C-A **
10004490-C-A 10166881-C-A **
11014931-C-A **
24904723-T-A 22758576-T-A g1 **
10884922-T-A **
6923079-G-T 7055038-G-T **
2806248-C-A 2938207-C-A Y81501 **
15127826-TA-T 13015913-TA-T **
20673814-T-C 18511928-T-C P4_Prx **
11018881-A-C **
15619435-C-A 13507555-C-A **
22277537-G-T 20115651-G-T FT454760 DYZ19 **
19719328-A-AC 17607448-A-AC P5_Prx **
19854727-T-TA 17742847-T-TA P5_Prx **
19854737-C-G 17742857-C-G P5_Prx **
17831146-C-A 15719266-C-A **
28500070-C-A 26353923-C-A **
10892550-T-C **
22995122-C-A 20833236-C-A **
10935588-AT-A **
13859389-G-C 11738683-G-C **
13859404-G-C 11738698-G-C **
13859424-G-GGAAGA 11738718-G-GGAAGA **
5194762-G-T 5326721-G-T **
9140086-C-A 9302477-C-A **
10892595-T-G **
10919083-G-T **
28640214-C-A 26494067-C-A **
10821836-C-G **
10844172-A-G **
21588308-G-T 19426422-G-T **
6593394-C-A 6725353-C-A **
25890544-A-AG 23744397-A-AG P1_Y1 **
10691289-T-G **
10791295-C-A **
10892537-C-T **
10892540-T-G **
10892544-A-AGCCATTCTG **
22244974-G-T 20083088-G-T DYZ19 **
17928997-C-A 15817117-C-A **
10892600-T-G **
13587861-AT-A 11432185-AT-A **
10753964-C-A **
17684338-C-A 15572458-C-A **
56752159-C-A **
6786898-T-G 6918857-T-G **
11018911-C-T **
17884473-G-T 15772593-G-T **
11648191-C-T **
21380474-C-A 19218588-C-A **
14355468-A-G 12234763-A-G **
10830869-C-A **
2708456-GAATA-G 2840415-GAATA-G **
3113877-G-C 3245836-G-C **
3267942-T-G 3399901-T-G **
3296131-G-C 3428090-G-C **
3334738-C-T 3466697-C-T **
3533187-G-T 3665146-G-T **
3650747-A-C 3782706-A-C **
3684498-A-G 3816457-A-G **
3962681-C-A 4094640-C-A **
4076877-G-T 4208836-G-T **
4142483-G-T 4274442-G-T **
4208967-A-T 4340926-A-T **
4286045-C-A 4418004-C-A **
4734392-A-G 4866351-A-G **
4804381-G-T 4936340-G-T **
5202393-A-G 5334352-A-G **
5231649-C-A 5363608-C-A **
5313494-T-G 5445453-T-G **
5449321-T-G 5581280-T-G **
5619651-C-T 5751610-C-T FT133085 **
6487885-A-G 6619844-A-G **
6654623-C-A 6786582-C-A **
7053929-C-A 7185888-C-A FT345144 **
7150320-C-A 7282279-C-A **
7301509-G-A 7433468-G-A **
7433943-T-C 7565902-T-C FT75775 **
8061728-G-T 8193687-G-T **
8094450-C-A 8226409-C-A **
8130513-C-A 8262472-C-A **
8735005-G-A 8866964-G-A **
9971492-A-G 10133883-A-G **
10652922-T-G **
10652975-C-A **
10691343-A-G **
10758026-A-T **
10763327-A-C **
10763352-C-G **
10764502-TC-T **
10764505-A-AT **
10764556-A-AT **
10764915-C-G **
10769833-C-G **
10769842-C-A **
10778266-C-CCAGTG **
10804920-CAAT-C **
10804926-T-TCTATTAGA **
10804945-A-T **
10804952-T-A **
10818182-C-A **
10821199-C-A **
10825422-C-T **
10830893-A-G **
10832976-T-A **
10839749-T-G **
10909825-G-T **
10912269-C-A **
10932582-C-A **
10932760-C-CAATAA **
10935592-C-CG **
10935608-AT-A **
10935632-C-A **
10940896-C-A **
10940899-T-A **
10983108-C-G **
10999858-C-CAACGCG **
10999861-T-TTGAG **
11004410-CA-C **
11004412-T-TC **
11025889-A-T **
13236153-G-A 11080477-G-A **
13251987-G-T 11096311-G-T **
13259074-C-A 11103398-C-A **
13434238-C-A 11278562-C-A **
13521270-C-A 11365594-C-A **
13604728-TTAGC-T 11449052-TTAGC-T **
14073187-C-CTTT 11952481-C-CTTT 27×T**
14293658-G-T 12172952-G-T **
14517644-C-A 12405845-C-A **
14605735-C-T 12493937-C-T **
14718098-G-T 12606166-G-T **
14815416-C-A 12703487-C-A **
15386694-T-G 13274814-T-G **
15798161-G-T 13686281-G-T **
16070661-G-A 13958781-G-A **
16466752-G-T 14354872-G-T **
16617505-G-T 14505625-G-T **
16676854-C-A 14564974-C-A **
16681557-CT-C 14569677-CT-C **
16990220-T-C 14878340-T-C **
17027584-C-A 14915704-C-A **
17056758-A-C 14944878-A-C **
17313574-C-A 15201694-C-A **
17402486-C-A 15290606-C-A **
17461985-A-G 15350105-A-G **
17605211-C-A 15493331-C-A **
17822052-TAGAA-T 15710172-TAGAA-T **
19248217-G-A 17136337-G-A **
19644753-T-C 17532873-T-C P5_Prx **
19854726-T-TA 17742846-T-TA P5_Prx **
19874562-T-G 17762682-T-G P5_Prx **
19925911-C-A 17814031-C-A P5_Prx **
20370172-T-TG 18208286-T-TG P5_Dst **
20420951-G-T 18259065-G-T P5_Dst **
21285273-C-A 19123387-C-A **
21540883-GT-G 19378997-GT-G **
22134131-G-C 19972245-G-C **
22798029-T-C 20636143-T-C **
22949888-T-TGTG 20788002-T-TGTG **
23339780-G-T 21177894-G-T **
24300720-C-A 22154573-C-A P3_t1 **
24466311-G-T 22320164-G-T **
26106370-T-G 23960223-T-G P1_Y1 **
26189737-A-C 24043590-A-C P1_Y1 **
26189760-G-GTT 24043613-G-GTT P1_Y1 21×T**
26499999-G-T 24353852-G-T P1_Y1 **
28497277-C-T 26351130-C-T **
28581189-A-G 26435042-A-G **
28632796-A-C 26486649-A-C **
28812215-G-C 26666068-G-C **
13483391-C-G 11327715-C-G ***
28802779-C-T 26656632-C-T FT462214 ***
21032982-C-A 18871096-C-A ***
7255062-C-A 7387021-C-A ***
3131664-G-T 3263623-G-T ***
10677690-G-T ***
16272254-C-A 14160374-C-A ***
5684767-C-A 5816726-C-A ***
11014332-C-A ***
15647993-G-A 13536113-G-A ***
16703874-G-A 14591994-G-A FT380860 ***
17143891-ATTTTTTTTTTT-A,AT 15032011-ATTTTTTTTTTT-A,AT 35×T***
21713438-TAA-T,TAAA 19551552-TAA-T,TAAA 16×A***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.