Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > S14469 > FGC8158 > FGC8154

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 STRFTDNA
16304328-CT-C 14192448-CT-C +
7268761-T-C 7400720-T-C FGC8148 YY+
15621598-A-G 13509718-A-G FGC8163 YY+
8968956-G-A 9131347-G-A +
8535306-C-A 8667265-C-A FGC8152 YY+
7614758-T-G 7746717-T-G FGC8151 YY+
14025561-GAAA-G 11904855-GAAA-G +
14025565-AG-A 11904859-AG-A +
7600076-T-C 7732035-T-C FGC8150 YY+
7535814-C-T 7667773-C-T FGC8149 YY+
6997483-G-A 7129442-G-A FGC8147 YY+
22457946-T-G 20296060-T-G ALK382 DYZ19 +
22189279-C-T 20027393-C-T FGC8171 YY+
21467574-C-T 19305688-C-T FGC8170 YY+
6870045-C-G 7002004-C-G FGC8146 YY+
18760206-C-A 16648326-C-A FGC8169 YY+
18219927-A-G 16108047-A-G FGC8168 Y+
17853213-G-C 15741333-G-C FGC8167 YY+
17153032-G-A 15041152-G-A FGC8166 YY+
16900458-C-T 14788578-C-T FGC8165 YY+
22457923-T-C 20296037-T-C DYZ19 +
15754202-C-A 13642322-C-A FGC8164 YY+
14983989-A-G 12872057-A-G FGC8159 YY+
22830407-C-T 20668521-C-T FGC8175 YY+
15517276-T-C 13405396-T-C FGC8162 YY+
24206848-T-C 22060701-T-C P3_b1 +
15022389-AT-A 12910478-AT-A 10×T+
23649359-T-A 21487473-T-A FGC8177 Y+
23463881-G-T 21301995-G-T FGC8176 YY+
22594999-T-C 20433113-T-C FGC8174 YY+
14809480-A-G 12697551-A-G FGC8157 YY+
22459959-G-A 20298073-G-A FGC8173 DYZ19 +
14224786-A-C 12104080-A-C FGC8156 YY+
15165240-T-C 13053326-T-C FGC8160 YY+
15360368-T-C 13248488-T-C FGC8161 YY+
8852858-C-A 8984817-C-A YY*
2681272-C-A 2813231-C-A YY*
9524124-CAT-C 9686515-CAT-C **
13249059-C-T 11093383-C-T **
16020260-G-T 13908380-G-T **
16640301-G-T 14528421-G-T CTS6053 **
13801051-A-G 11680345-A-G **
13801064-G-GAATGGAGATT 11680358-G-GAATGGAGATT **
6931265-C-A 7063224-C-A **
25767725-T-G 23621578-T-G P1_b3 **
19411913-GAAA-G 17300033-GAAA-G **
19411917-AG-A 17300037-AG-A **
13801046-G-T 11680340-G-T **
13801045-A-G 11680339-A-G **
23144301-G-T 20982415-G-T **
15027510-A-C 12915598-A-C **
13866812-A-G 11746106-A-G ***
19910967-C-T 17799087-C-T P5_Prx ***
16945883-TAA-T,TA 14834003-TAA-T,TA 15×A***
22458007-T-C 20296121-T-C DYZ19 ***
28794028-G-C 26647881-G-C ***
26286116-ATT-A 24139969-ATT-A P1_Y1 ***
26114789-AT-A 23968642-AT-A P1_Y1 ***
25936681-G-A 23790534-G-A P1_Y1 ***
25728480-T-C 23582333-T-C P1_b3 ***
25130794-T-C 22984647-T-C g1 ***
25010021-G-C 22863874-G-C g1 ***
24162965-C-T 22016818-C-T P3_b1 ***
22459517-T-G 20297631-T-G FGC8172 DYZ19 ***
22458017-A-C 20296131-A-C DYZ19 ***
22458011-G-A 20296125-G-A DYZ19 ***
22457999-T-G 20296113-T-G DYZ19 ***
13863279-G-T 11742573-G-T ***
22427229-A-T 20265343-A-T DYZ19 ***
22422996-A-T 20261110-A-T DYZ19 ***
22321660-G-C 20159774-G-C DYZ19 ***
22308719-G-C 20146833-G-C DYZ19 ***
22307355-C-G 20145469-C-G DYZ19 ***
22305840-A-C 20143954-A-C DYZ19 ***
22288486-G-C 20126600-G-C DYZ19 ***
22283443-G-C 20121557-G-C DYZ19 ***
22266066-G-A 20104180-G-A DYZ19 ***
22262140-C-G 20100254-C-G DYZ19 ***
22243906-G-A 20082020-G-A DYZ19 ***
13863386-C-A 11742680-C-A ***
13647944-T-C 11492268-T-C ***
13859362-G-GTGGAA 11738656-G-GTGGAA ***
13806253-C-G 11685547-C-G ***
13710152-T-A 11554476-T-A ***
13801166-A-T 11680460-A-T ***
13810177-TGGATA-T,TGGAAT 11689471-TGGATA-T,TGGAAT ***
13483229-C-G 11327553-C-G ***
13695999-G-A 11540323-G-A ***
13863371-C-A 11742665-C-A ***
13648877-T-A 11493201-T-A ***
13648876-A-C 11493200-A-C ***
22308782-A-T 20146896-A-T DYZ19 ***
13142082-G-A 10631568-G-A ***
13817965-C-A 11697259-C-A ***
13801158-G-C 11680452-G-C ***
13835396-C-A 11714690-C-A ***
19682353-GAAA-G 17570473-GAAA-G P5_Prx ***
9190580-G-C 9352971-G-C ***
13868818-C-A 11748112-C-A ***
13805306-A-C,T 11684600-A-C,T ***
13865878-T-A 11745172-T-A ***
13137869-C-T 10627355-C-T ***
13451511-C-T 11295835-C-T ***
9991637-C-CA 10154028-C-CA 20×T***
9959870-T-C 10122261-T-C ***
13454172-G-C 11298496-G-C ***
13867904-A-G 11747198-A-G ***
58975920-T-C 56829773-T-C ***
22336309-A-T 20174423-A-T DYZ19 ***
13710164-G-A 11554488-G-A ***
19682358-AG-A 17570478-AG-A P5_Prx ***
13857540-CAGATGGAATG-T 11736834-CAGATGGAATG-T ***
13865840-C-A,G 11745134-C-A,G ***
13853050-A-T 11732344-A-T ***
13838081-C-G 11717375-C-G ***
13700543-C-G,T 11544867-C-G,T ***
13664543-C-CCAATG 11508867-C-CCAATG ***
13847319-G-A 11726613-G-A ***
13647943-A-G 11492267-A-G ***
13647940-G-A 11492264-G-A ***
13647938-T-TTGCAA 11492262-T-TTGCAA ***
13137402-G-C,T 10626888-G-C,T ***
9307584-G-C 9469975-G-C ***
6347812-AAG-A,GAA 6479771-AAG-A,GAA ***
22147730-CTTTCT-A,C 19985844-CTTTCT-A,C 19×TTTCT***
13809659-C-T 11688953-C-T ***
22359529-T-A 20197643-T-A DYZ19 ***
22358169-G-T 20196283-G-T DYZ19 ***
13817988-G-A 11697282-G-A ***
13679952-GAATGGAATCA-G 11524276-GAATGGAATCA-G ***
13451506-C-T 11295830-C-T ***
13703875-A-G 11548199-A-G ***
24417009-AG-A 22270862-AG-A ***
13724052-G-T 11568376-G-T ***
5409735-TC-T 5541694-TC-T ***
3640987-T-TCC 3772946-T-TCC 11×TTTCC***
3640986-C-CTTT 3772945-C-CTTT ***
16242632-T-TCTATCTA 14130752-T-TCTATCTA 10×TCTA***
13734467-G-A 11578791-G-A ***
58972870-A-T 56826723-A-T ***
58977985-T-C 56831838-T-C ***

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.

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