FGA

CODIS Core

FGA is a tetranucleotide short tandem repeat (STR) locus on chromosome 4 (4q31.3), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

4q31.3

STRNaming template (FSSG)

GAAG[1]AAAG[1]GAAG[2]GAG[1]AAAG[n]AGAAA[1]AAAG[3]

Type

Tetranucleotide

Reference Allele

Explore internal sequence structure

See how the STRNaming name of the reference allele maps onto its sequence: repeat blocks, flanking regions and flanking variants.

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See the reads at this locus

Open the built-in IGV viewer on the hg38 window of this marker with a 1000 Genomes sample.

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Genomic Coordinates

GRCh38/hg38

Repeat region

chr4:154,587,736-154,587,823 (88 bp)

GRCh37/hg19

Repeat region

chr4:155,508,888-155,508,975 (88 bp)

Motif and sequences are shown on the forward (+) strand of GRCh38.

Sequence structure (FSSG)

ISFG minimum range, bracketing and kit coverage from the Forensic Sequence Structure Guide, FSSG v6.1 (STRidER; distributed as FSSG_v6-1_beta.xlsx).

STRNaming Formatted ISFG Minimum Range for Common Alleles (FSSG)

GAAG[1]AAAG[1]GAAG[2]GAG[1]AAAG[n]AGAAA[1]AAAG[3]

GAAG[1]AAAG[1]GAAG[2]GAG[1]AAAG[5]AAGG[1]AAAG[n]AGAAA[1]AAAG[3]

GAAG[1]AAAG[1]GAAG[2]GAG[1]AAAG[n]AAA[1]AAAG[3]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE22_GAAG[1]AAAG[1]GAAG[2]GAG[1]AAAG[14]AGAAA[1]AAAG[3]

Historical bracketing (2016-2023)

[GGAA]2 GGAG [AAAG]14 AGAA AAAA [GAAA]3

ISFG minimum range (GRCh38)

chr4:154,587,729-154,587,827 (99 bp)

MPS kits covering this locus

PowerSeq 46GY (Does not cover the whole ISFG minimum range.)
ForenSeq Signature Prep/Plus and MainstAY
Precision ID GlobalFiler NGS STR Panel v2
IDSeek OmniSTR Global (Does not cover the whole ISFG minimum range.)

Kit range does not cover the whole ISFG minimum range of this locus (chr4:154,587,729-154,587,827), according to the kit ranges in the FSSG. Bases of the minimum range outside a kit's range are not sequenced by that kit; bases filled in from the reference should be identified as such.

Notes from the FSSG

PowerSeq 46GY range shown is exclusive of primer, inferred bases may be included in GeneMarker HTS v2.6.1 output. Originally characterized on the reverse strand

Allele frequencies at a glance

Most common allele per population group, with its frequency and the sample size, in the capillary electrophoresis data of pop.STR / SP-SMART.

Africa: Allele 22 (0.211, n = 504)
Native American: Allele 22 (0.171, n = 535)
East Asia: Allele 23 (0.224, n = 219)
Central and South Asia: Allele 24 (0.219, n = 192)
Europe: Allele 22 (0.187, n = 2,102)
Middle East: Allele 23 (0.195, n = 159)
Oceania: Allele 24 (0.250, n = 20)

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.
Allele	AFR	NAM	EAS	CSA	EUR	MES	OCE
16	0.001	0	0	0	0	0	0
17	0	0	0	0	0.001	0.006	0
17.2	0	0	0	0	0.001	0	0
18	0.017	0.007	0.021	0.016	0.015	0.006	0
18.2	0	0.007	0	0	0.003	0.003	0
19	0.018	0.075	0.034	0.042	0.063	0.047	0.100
19.2	0.001	0.001	0	0.003	0.001	0.003	0
20	0.020	0.079	0.078	0.078	0.107	0.069	0.025
20.2	0	0	0.002	0	0.001	0	0
20.3	0	0.001	0	0	0	0	0
21	0.081	0.136	0.116	0.128	0.154	0.182	0.075
21.2	0.002	0.001	0.002	0	0.001	0.009	0
22	0.211	0.171	0.146	0.164	0.187	0.167	0.100
22.2	0.002	0.002	0.005	0.016	0.007	0	0
23	0.197	0.136	0.224	0.133	0.154	0.195	0.150
23.2	0	0	0.005	0.005	0.003	0	0
23.3	0.015	0	0	0	0	0	0
24	0.166	0.165	0.196	0.219	0.142	0.167	0.250
24.2	0	0	0.009	0.010	0	0	0
24.3	0.006	0	0	0.003	0	0	0
25	0.108	0.123	0.078	0.141	0.091	0.091	0.200
25.2	0	0	0.007	0.010	0.001	0	0
26	0.045	0.051	0.064	0.023	0.042	0.038	0.050
27	0.023	0.022	0.007	0.005	0.016	0.003	0
27.1	0	0	0	0	0	0	0.025
27.2	0	0	0.002	0	0	0	0
28	0.052	0.011	0.005	0.003	0.004	0.009	0
28.1	0	0	0	0	0	0	0.025
29	0.023	0.006	0	0.003	0.002	0.003	0
30	0.009	0.002	0	0	0.001	0	0
30.2	0	0	0	0	0.001	0	0
31.2	0.002	0	0	0	0	0	0
33	0	0.001	0	0	0	0	0
33.3	0.001	0	0	0	0	0	0
43.2	0.001	0	0	0	0	0	0
45.2	0	0.003	0	0	0	0	0
46.2	0	0.001	0	0	0	0	0

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.

Variant Alleles

STRbase reports 140 sequence variants across 41 allele designations.

16.2

17.2

18.2

19.2

20.2

21.2

22.2

22.3

23.1

23.2

23.3

24.2

24.3

25.2

26.2

27.1

27.2

28.1

29.2

30.2

31.2

32.2

42.2

43.2

44.2

46.2

Related markers

Other STR markers on chromosome 4

D4S2408

Other CODIS core loci

Browse the full STR marker catalog