Table of Contents
PGD: old versions
- root element: <PGD>
- microsat data are number of repeats
- nucleotid data: just one loci in one tag (popLoci/ indLoci)! (If more than one loci: repeat the whole ind tag for every loci)
- stylesheet: stylesheet_data-format3.pdf
1. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | number_samples | x | x | x | x | x | x | ||
data_type | x | x | x | x | x | x | |||
number_loci | number | x | x | x | x | x | |||
loci (attribute: name) | locations | o | o | o | o | o | |||
length | o | o | o | o | o | ||||
missing | o | o | o | o | o | ||||
gap | o | o | o | o | o | ||||
gametic_phase | o | o | o | o | o | ||||
recessive_alleles | o | o | o | o | o | ||||
sample (attribute: name) | size | x | x | x | x | x | x | ||
id (attribute: name) | frequency | x | x | x | x | x | x | ||
loci (attribute: name) (when unaligned) | position | o | o | o | |||||
genotype/haplotype (a) | x(a) | x(a) | x(a) | ||||||
genotype/haplotype (a) (attribute: name) (when aligned) | x | x(a) | x(a) | x | x(a) | ||||
structure (attribute: name) | number_groups | o | o | o | o | o | |||
group (attribute: name) (sample name, sample name) | o | o | o | o | o | ||||
distance_matrix (attribute: name) | size | o | o | o | o | o | |||
lables | o | o | o | o | o | ||||
matrix | o | o | o | o | o |
x: obligatory
o: optional
a: alternative
2. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | number_population | x | x | x | x | x | x | ||
data_type | x | x | x | x | x | x | |||
number_loci* | number | x | x | x | x | x | |||
loci (attribute: name) | locations | o | o | o | o | o | |||
length | o | o | o | o | o | ||||
missing | o | o | o | o | o | ||||
gap | o | o | o | o | o | ||||
gametic_phase | o | o | o | o | o | ||||
recessive_alleles | o | o | o | o | o | ||||
population (attribute: name) | size | x | x | x | x | x | x | ||
geographic_coord | o | o | o | o | o | o | |||
id (attribute: name) (a3) | frequency | x | x | x | x | x | x | ||
loci (attribute: name) (when unaligned) | location | o | o | o | |||||
begin | o | o | o | ||||||
length | o | o | o | ||||||
genotype/haplotype (a1) | x (a1) | x (a1) | x (a1) | ||||||
genotype/haplotype (a1) (attribute: name) (when aligned) | x | x (a1) | x (a1) | x | x (a1) | ||||
ind (attribute: name) (a3) | geographic_coord | o | o | o | o | o | o | ||
loci (attribute: name) (when unaligned) | location | o | o | o | |||||
begin | o | o | o | ||||||
length | o | o | o | ||||||
genotype/haplotype (a2) | x (a2) | x (a2) | x (a2) | ||||||
genotype/haplotype (a2) (attribute: name) (when aligned) | x | x (a2) | x (a2) | x | x (a2) | ||||
structure (attribute: name) | number_groups | o | o | o | o | o | |||
group (attribute: name) (sample name, sample name) | o | o | o | o | o | ||||
distance_matrix (attribute: name) | size | o | o | o | o | o | |||
lables | o | o | o | o | o | ||||
matrix | o | o | o | o | o |
* when for all populations the same
x: obligatory
o: optional
a: alternative to
3. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | number_populations | x | x | x | x | x | x | ||
data_type | x | x | x | x | x | x | |||
number_loci * | number | x | x | x | x | x | |||
loci (attribute: name) | location | o | o | o | o | o | |||
length | o | o | o | o | o | ||||
gene_copies * | x | x (a1) | x (a1) | x | x (a1) | ||||
aligned | x | x | x | x | x | ||||
genotypic_data | x | x | x | x | x | ||||
missing | x | x | x | x | x | ||||
gap | x | x | x | x | x | ||||
gametic_phase | o | o | o | o | o | ||||
recessive_alleles | o | o | o | o | o | ||||
population (attribute: name) | size | x | x | x | x | x | x | ||
geographic_coord | o | o | o | o | o | o | |||
linguistic_group | o | o | o | o | o | o | |||
id (attribute: name) (a3) | frequency | x | x | x | x | x | x | ||
genotype/haplotype (attribute: name) | x | x | x | x | x | ||||
ind (attribute: name) (a3) | geographic_coord | o | o | o | o | o | |||
linguistic_group | o | o | o | o | o | ||||
loci (attribute: name) (when unaligned) | location | o | o | o | |||||
begin | o | o | o | ||||||
length | o | o | o | ||||||
gene_copies | x (a1) | x (a1) | x (a1) | ||||||
genotype/haplotype (a2) | x (a2) | x (a2) | x (a2) | ||||||
genotype/haplotype (a2) (attribute: name) (when aligned) | x | x (a2) | x (a2) | x | x (a2) | ||||
structure (attribute: name) | number_groups | o | o | o | o | o | o | ||
group (attribute: name) (sample name, sample name, …) | o | o | o | o | o | o | |||
distance_matrix (attribute: name) | size | o | o | o | o | o | o | ||
labels | o | o | o | o | o | o | |||
matrix (number (line break) number, number (line break)…) | o | o | o | o | o | o |
* when for all populations the same
x: obligatory
o: optional
a: alternative to
4. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | number_populations | x | x | x | x | x | x | ||
data_type | x | x | x | x | x | x | |||
number_loci * | number | x | x | x | x | x | |||
loci (attribute: name) | location | o | o | o | o | o | |||
length | o | o | o | o | o | ||||
number_strains * | x | x (a1) | x (a1) | x | x (a1) | ||||
aligned | x | x | x | x | x | ||||
genotypic_data | x | x | x | x | x | ||||
missing | x | x | x | x | x | ||||
gap | x | x | x | x | x | ||||
gametic_phase | o | o | o | o | o | ||||
recessive_alleles | o | o | o | o | o | ||||
population (attribute: name) aligned (a2) | size | x | x | x | x | x | x | ||
geographic_coord * | o (a4) | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
linguistic_group * | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | o | |||
number_strains * | o (a1) | o (a1) | o (a1) | o (a1) | o (a1) | ||||
id (attribute: name) (a3) | frequency | x | x | x | x | x | x | ||
genotype/haplotype (attribute: name) (loci, loci,…) | x | x | x | x | x | ||||
ind (attribute: name) (a3) | geographic_coord | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
linguistic_group | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | ||||
number_strains | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
genotype/haplotype (attribute: name) (loci, loci,…) | x | x | x | x | x | ||||
population (attribute: name) unaligned (a2) | size | x | x | x | |||||
geographic_coord * | o (a6) | o (a6) | o (a6) | ||||||
linguistic_group * | o (a7) | o (a7) | o (a7) | ||||||
loci_location (attribute: name) * | o (a8) | o (a8) | o (a8) | ||||||
number_strains * | o (a9) | o (a9) | o (a9) | ||||||
ind (attribute: name) | geographic_coord | o (a6)*3 | o (a6)*3 | o (a6)*3 | |||||
linguistic_group | o (a7)*3 | o (a7)*3 | o (a7)*3 | ||||||
loci_location (attribute: name)*2 | o (a8)*3 | o (a8)*3 | o (a8)*3 | ||||||
number_strains | x (a9) | x (a9) | x (a9) | ||||||
strain (attribute: name) | begin | x | x | x | |||||
length | x | x | x | ||||||
genotype/haplotype | x | x | x | ||||||
structure (attribute: name) (o) | number_groups | x | x | x | x | x | x | ||
group (attribute: name) (sample name, sample name, …) | x | x | x | x | x | x | |||
distance_matrix (attribute: name) (o) | size | x | x | x | x | x | x | ||
labels | x | x | x | x | x | x | |||
matrix (number (line break) number, number (line break)…) | x | x | x | x | x | x |
* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population
*3 if for one individual defined, it has to be defined for all individuals
x: obligatory
o: optional
a: alternative to
5. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | nb_pop | x | x | x | x | x | x | ||
data_type | x | x | x | x | x | x | |||
loci (o) * | nb | x | x | x | x | x | |||
locus (attribute: id) | location | x | x | x | x | x | |||
length | o | o | o | o | o | ||||
links | o | o | o | o | o | ||||
nb_reads * | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
aligned | x | x | x | x | x | ||||
geno_data | x | x | x | x | x | ||||
missing | x | x | x | x | x | ||||
gap | x | x | x | x | x | ||||
gametic_phase | o | o | o | o | o | ||||
recessive_alleles | o | o | o | o | o | ||||
loci (o) | nb | x | x | x | x | x | |||
locus (attribute: id) | location | x | x | x | x | x | |||
length | o | o | o | o | o | ||||
links | o | o | o | o | o | ||||
population (attribute: name) aligned, same data type (a2) | size | x | x | x | x | x | x | ||
geo_coord * | o (a4) | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
linguistic_group * | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | o | |||
nb_reads * | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
loci (locus, locus,…) * | x | x | x | x | x | ||||
id (attribute: name) (a3) | freq | x | x | x | x | x | x | ||
geno/hap (attribute: name) (locus, locus,…) | x | x | x | x | x | ||||
ind (attribute: name) (a3) | geo_coord | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
linguistic_group | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | ||||
nb_reads | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
geno/hap (attribute: name) (locus, locus,…) | x | x | x | x | x | ||||
population (attribute: name) unaligned (a2) | size | x | x | x | |||||
geo_coord * | o (a6) | o (a6) | o (a6) | ||||||
linguistic_group * | o (a7) | o (a7) | o (a7) | ||||||
locus (attribute: id)* | o (a8) | o (a8) | o (a8) | ||||||
nb_reads * | o (a9) | o (a9) | o (a9) | ||||||
ind (attribute: name) | geo_coord | o (a6)*3 | o (a6)*3 | o (a6)*3 | |||||
linguistic_group | o (a7)*3 | o (a7)*3 | o (a7)*3 | ||||||
locus (attribute: id)*2 | o (a8)*3 | o (a8)*3 | o (a8)*3 | ||||||
nb_reads | x (a9) | x (a9) | x (a9) | ||||||
read (attribute: name) | start | x | x | x | |||||
length | x | x | x | ||||||
geno/hap | x | x | x | ||||||
structure (attribute: name) (o) | number_groups | x | x | x | x | x | x | ||
group (attribute: name) (sample name, sample name, …) | x | x | x | x | x | x | |||
distance_matrix (attribute: name) (o) | size | x | x | x | x | x | x | ||
labels | x | x | x | x | x | x | |||
matrix (number (line break) number, number (line break)…) | x | x | x | x | x | x |
* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population
*3 if for one individual defined, it has to be defined for all individuals
x: obligatory
o: optional
a: alternative to
6. version:
data type | |||||||||
---|---|---|---|---|---|---|---|---|---|
block | subtags | standard | DNA | SNP | Microsattelite | RFLP (AFLP) | Allel frequency | ||
header (attribute: title) | organism | o | o | o | o | o | o | ||
numPop | x | x | x | x | x | x | |||
numReads * | x | x | x | x | x | ||||
aligned | x | x | x | x | x | ||||
missing | x | x | x | x | x | ||||
gap | x | x | x | x | x | ||||
gameticPhase | o | o | o | o | o | ||||
recessiveData | o | o | o | o | o | ||||
loci (o) | lociNum | x | x | x | x | x | |||
lociDataType * | x (a10) | x (a10) | x (a10) | x (a10) | x (a10) | x | |||
locus (attribute: id) | locusDataType | a10 | a10 | a10 | a10 | a10 | |||
locusChromosom | o | o | o | o | o | ||||
locusLocation | o | o | o | o | o | ||||
locusGenic | o | o | o | o | o | ||||
locusLength | o | o | o | o | o | ||||
locusLinks | o | o | o | o | o | ||||
locusComments | o | o | o | o | o | ||||
population (attribute: name) aligned, same data type (a2) | popSize | x | x | x | x | x | x | ||
popGeogCoord * | o (a4) | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
popLingGroup * | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | o | |||
popNumReads * | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
popLoci (locus, locus,…) * | x | x | x | x | x | ||||
ind (attribute: name) (a3) | indGeogCoord | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
indLingGroup | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | ||||
indNumReads | a1 | a1 | a1 | a1 | a1 | ||||
indFreq (absolute Freq) | o | o | o | o | o | x | |||
data (locus, locus,…) | x | x | x | x | x | ||||
population (attribute: name) aligned, diff data type (a2) | popSize | x | x | x | x | x | |||
popGeogCoord * | o (a4) | o (a4) | o (a4) | o (a4) | o (a4) | ||||
popLingGroup * | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | ||||
popNumReads * | x (a1) | x (a1) | x (a1) | x (a1) | x (a1) | ||||
ind (attribute: name) (a3) | indGeogCoord | o (a4) | o (a4) | o (a4) | o (a4) | o | |||
indLingGroup | o (a5) | o (a5) | o (a5) | o (a5) | o (a5) | ||||
indLoci (locus, locus,…) | x | x | x | x | x | ||||
indNumReads | a1 | a1 | a1 | a1 | a1 | ||||
indFreq (absolute Freq) | o | o | o | o | o | x | |||
data (locus, locus,…) | x | x | x | x | x | ||||
population (attribute: name) unaligned (a2) | popSize | x | |||||||
popGeogCoord * | o (a6) | ||||||||
popLingGroup * | o (a7) | ||||||||
popNumReads * | x (a9) | ||||||||
popLocus * | o (a8) | ||||||||
ind (attribute: name) | indGeogCoord | o (a6) | |||||||
indLingGroup | o (a7) | ||||||||
indLocus *2 | o (a8) | ||||||||
indFreq (absolute Freq) | o | ||||||||
indNumReads | a9 | ||||||||
read | start | x (if unalig.) | |||||||
length | o | ||||||||
data | x | ||||||||
structure (attribute: name) (o) | numGroups | x | x | x | x | x | x | ||
group (attribute: name) (sample name, sample name, …) | x | x | x | x | x | x | |||
distanceMatrix (attribute: name) (o) | matrixSize | x | x | x | x | x | x | ||
matrixLabels (name, name,…) | x | x | x | x | x | x | |||
matrix (number (line break) number, number (line break)…) | x | x | x | x | x | x |
* when for all populations/individuals the same
*2 if it exist –> align DNA over one individual, if it not exist –> align DNA over one population
x: obligatory
o: optional
a: alternative to