Perdue

BigY3: 172358, FTDNA: 172358

Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF63/S522 > BY592 > BY38638

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 STRBigY3
172358		FTDNA
172358
4760111-C-A 4892070-C-A A+
20243436-C-T 18081550-C-T FGC42219 P5_Dst A*
6302706-T-G 6434665-T-G IR3_Dst A****
6305434-T-G 6437393-T-G IR3_Dst A****
18285602-T-G 16173722-T-G P6_Prx A****
19613805-G-A 17501925-G-A P5_Prx YA****
19617456-T-A 17505576-T-A P5_Prx YA****
19701126-G-A 17589246-G-A P5_Prx A****
19833219-C-T 17721339-C-T P5_Prx A****
22313651-G-A 20151765-G-A DYZ19 A****
25927975-G-A 23781828-G-A P1_Y1 A****
10776512-C-G A*
28817570-A-G 26671423-A-G A*
13450815-C-T 11295139-C-T A*
6307320-C-T 6439279-C-T IR3_Dst A*
16109080-G-A 13997200-G-A P8_Prx A*
18502473-T-C 16390593-T-C P6_Dst A*
19808747-G-A 17696867-G-A P5_Prx A*
26361395-T-A 24215248-T-A P1_Y1 A*
56836147-A-AT A*
14168709-A-T 12048003-A-T Y14321 Z27507 YY+
16548244-T-G 14436364-T-G F351 AM00257 AMM212 YY++
6677826-A-G 6809785-A-G BY60694 YY++
7018374-G-A 7150333-G-A MF2947 Y++
7669615-C-T 7801574-C-T BY66696 YY++
7973612-G-GT 8105571-G-GT ***+
8070210-G-A 8202169-G-A BY69729 YY++
8304807-C-T 8436766-C-T BY71540 YY++
8367042-A-G 8499001-A-G BY72044 YY++
8682961-A-AT 8814920-A-AT 9×T*+
9491416-G-T 9653807-G-T BY79880 ++
13659226-G-A 11503550-G-A BY156197 ++
14140184-C-T 12019478-C-T BY93281 YY++
14222301-G-C 12101595-G-C BY94037 YY++
14931133-GC-G 12819198-GC-G ++
16545569-T-C 14433689-T-C BY108509 YY**+
16940799-T-G 14828919-T-G BY111271 YY++
17359528-T-G 15247648-T-G BY114157 YY++
17370076-T-C 15258196-T-C BY114261 YY++
17764056-T-C 15652176-T-C BY117236 YY++
18605964-C-A 16494084-C-A BY122530 YY++
19189670-G-A 17077790-G-A BY127080 YY**+
19525831-G-T 17413951-G-T BY129802 YY++
20828526-A-C 18666640-A-C BY163490 P4_Gap ++
21162223-A-G 19000337-A-G BY130783 YY++
21163528-C-A 19001642-C-A BY130788 YY++
21253311-G-GA 19091425-G-GA ***+
21306159-C-A 19144273-C-A BY131932 YY**+
21821904-A-G 19660018-A-G BY135718 YY++
22038594-A-T 19876708-A-T BY137255 YY++
22039607-C-A 19877721-C-A BY137266 YY**+
22262800-T-A 20100914-T-A BY163472 DYZ19 ++
22810539-C-A 20648653-C-A BY140929 Y+**
25205830-A-G 23059683-A-G g1 +
14425471-C-T 12304746-C-T FT83627 YY+
22871356-G-T 20709470-G-T FT84109 YY+
3462773-C-T 3594732-C-T FT82500 +
4060066-G-T 4192025-G-T FT82698 +
5033372-C-A 5165331-C-A FT82974 +
5221633-T-C 5353592-T-C FT83019 +
5258260-T-C 5390219-T-C FT83033 +
5738969-A-C 5870928-A-C FT83167 +
7211409-G-A 7343368-G-A FT83385 YY+
8854234-T-G 8986193-T-G FT83461 YY+
9952127-G-A 10114518-G-A FT373427 Y+
13643754-A-T 11488078-A-T FT446974 +
13693749-GAATGGAATGGCATGGCATGT-G 11538073-GAATGGAATGGCATGGCATGT-G +
13943765-T-A 11823059-T-A FT83546 Y+
15400101-G-A 13288221-G-A FT83698 Y+
16725503-G-A 14613623-G-A FT83808 Y+
17306818-G-GA 15194938-G-GA +
17916115-G-A 15804235-G-A FT83889 YY+
19251587-A-C 17139707-A-C FT83962 YY+
19259142-T-A 17147262-T-A FT83964 YY+
19631356-G-T 17519476-G-T BY163492 P5_Prx +
28693557-C-T 26547410-C-T FT84225 +
3194030-C-T 3325989-C-T *
9398688-G-A 9561079-G-A BY156081 ****
24071058-G-A 21924911-G-A Z9835 P3_b1 **
14792841-G-T 12680912-G-T **
9398681-T-C 9561072-T-C BZ2917 ****
9398683-A-G 9561074-A-G BZ2918 ****
9398685-A-G 9561076-A-G BZ2919 ****
18210273-T-A 16098393-T-A A3430 *****
3436338-A-ATT 3568297-A-ATT **
6698832-G-A 6830791-G-A 12×T**
4763468-C-CA 4895427-C-CA 25×A**
5223302-C-CAA 5355261-C-CAA 16×A**
3062010-G-A 3193969-G-A **
3746566-G-C 3878525-G-C **
4008180-A-G 4140139-A-G **
4555697-T-C 4687656-T-C **
7128097-C-G 7260056-C-G **
8379366-CTTTTTTCTTT-C 8511325-CTTTTTTCTTT-C **
8812862-T-C 8944821-T-C **
9666512-A-G 9828903-A-G IR3_Prx **
13506523-A-G 11350847-A-G **
14047638-C-T 11926932-C-T **
14720258-A-G 12608326-A-G **
15185600-A-G 13073686-A-G **
15287430-G-A 13175529-G-A **
15477372-TA-T 13365492-TA-T **
17484716-C-A 15372836-C-A **
17728434-A-G 15616554-A-G **
19022337-C-T 16910457-C-T FT10408 **
19138245-A-G 17026365-A-G **
19138579-CTATA-C 17026699-CTATA-C **
19352425-T-G 17240545-T-G **
19677781-A-C 17565901-A-C P5_Prx **
20539884-T-TC 18377998-T-TC P5_Dst **
21122526-T-A 18960640-T-A **
22732747-G-A 20570861-G-A **
56699852-A-AGTGGG **
24312912-A-G 22166765-A-G P3_t1 ***
58975842-C-G 56829695-C-G ***
9311672-C-T 9474063-C-T ***
22285075-C-T 20123189-C-T DYZ19 ***
14610872-C-CATAG 12499074-C-CATAG ***
22316063-G-T 20154177-G-T DYZ19 ******
14610884-C-G 12499090-C-G ***
22240111-T-A 20078225-T-A DYZ19 ***
22240356-T-A 20078470-T-A DYZ19 ***
22255002-A-T 20093116-A-T DYZ19 ***
22431007-A-T 20269121-A-T DYZ19 ******
22476375-G-T 20314489-G-T FT459854 DYZ19 ******
22508699-G-C 20346813-G-C DYZ19 ***
24172459-C-T 22026312-C-T P3_b1 ***
24809879-C-G 22663732-C-G P3_b2 ***
24831502-C-A 22685355-C-A P3_b2 ***
24978570-T-C 22832423-T-C g1 ***
25222410-C-T 23076263-C-T P2_r1 ***
25862272-AT-A 23716125-AT-A P1_Y1 ***
26185711-TA-T 24039564-TA-T P1_Y1 ***
2835607-CT-C,CTT 2967566-CT-C,CTT 16×T***
15753178-CTTT-C,CTT 13641298-CTTT-C,CTT 20×T***
5252635-TAA-T 5384594-TAA-T 11×A***
3128625-CA-C,CAA 3260584-CA-C,CAA 20×A***
3350589-TA-T 3482548-TA-T ***
3874524-T-A 4006483-T-A ***
4521463-A-G 4653422-A-G ***
4826188-G-A 4958147-G-A ***
6468926-T-TAAA 6600885-T-TAAA 28×A***
8112217-C-T 8244176-C-T ***
8462088-AAA-T 8594047-AAA-T ***
9439897-CATAT-C 9602288-CATAT-C ***
9995052-C-G 10157443-C-G FT426724 ***
13390142-T-G 11234466-T-G ***
13466002-AG-A,CA 11310326-AG-A,CA ***
14088328-G-GTA 11967622-G-GTA ***
14825824-CT-C,CTTT 12713891-CT-C,CTTT 18×T***
14995161-A-T 12883246-A-T ***
15184124-G-T 13072210-G-T ***
16727723-T-C 14615843-T-C ***
18688500-CAA-C,CAAA 16576620-CAA-C,CAAA 20×A***
19275146-C-T 17163266-C-T ***
23419646-T-C 21257760-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.