family · mtDNA statistics

Agamidae

4 species in 4 genera. Every region of their mitochondrial genomes, side by side.

Group

species

41.6%

mean GC, whole genome

SD 1.1, range 40.3–43.0%

16,711

median genome length, bp

Range 16,129–16,761 bp

genera

Regions

GC content of each region across Agamidae, % of A + C + G + T

Parameter

Chart

GC % of every region
Region
Whole genome	4	41.64%	1.15	0.028	40.26%Calotes versicolor	41.63%	43.04%Pogona vitticeps	–	–
Protein-coding	4	41.81%	0.90	0.021	41.13%Calotes versicolor	41.54%	43.04%Pogona vitticeps	–	–
All rRNA	4	44.25%	0.90	0.020	43.53%Calotes versicolor	43.96%	45.53%Pogona vitticeps	–	–
All tRNA	4	41.85%	0.56	0.013	41.16%Hydrosaurus amboinensis	41.86%	42.52%Pogona vitticeps	–	–
12S rRNA	4	47.14%	3.63	0.077	43.15%Calotes versicolor	47.05%	51.32%Pogona vitticeps	–	–
16S rRNA	4	42.49%	1.43	0.034	40.68%Chlamydosaurus kingii	42.78%	43.73%Calotes versicolor	–	–
D-loop	4	35.28%	5.75	0.163	27.26%Calotes versicolor	37.13%	39.62%Pogona vitticeps	–	–
ND1	4	41.74%	1.50	0.036	39.86%Calotes versicolor	41.85%	43.42%Pogona vitticeps	–	–
ND2	4	41.77%	0.91	0.022	40.76%Calotes versicolor	41.67%	42.97%Pogona vitticeps	–	–
COX1	4	43.95%	1.50	0.034	42.22%Calotes versicolor	44.05%	45.48%Pogona vitticeps	–	–
COX2	4	41.84%	1.25	0.030	40.00%Chlamydosaurus kingii	42.30%	42.73%Pogona vitticeps	–	–
ATP8	4	39.03%	3.81	0.098	35.90%Chlamydosaurus kingii	37.99%	44.23%Pogona vitticeps	–	–
ATP6	4	40.57%	2.68	0.066	37.28%Chlamydosaurus kingii	40.62%	43.78%Pogona vitticeps	–	–
COX3	4	43.56%	0.89	0.020	42.47%Pogona vitticeps	43.56%	44.64%Hydrosaurus amboinensis	–	–
ND3	4	43.47%	0.70	0.016	42.86%Chlamydosaurus kingii	43.44%	44.13%Calotes versicolor	–	–
ND4L	4	38.83%	4.64	0.119	35.74%Calotes versicolor	36.94%	45.70%Hydrosaurus amboinensis	–	–
ND4	4	40.67%	0.67	0.016	40.00%Calotes versicolor	40.69%	41.29%Hydrosaurus amboinensis	–	–
ND5	4	40.89%	1.35	0.033	40.00%Calotes versicolor	40.36%	42.87%Pogona vitticeps	–	–
ND6	4	41.29%	3.00	0.073	36.97%Hydrosaurus amboinensis	42.14%	43.91%Chlamydosaurus kingii	–	–
CYTB	4	41.92%	1.16	0.028	40.92%Chlamydosaurus kingii	41.59%	43.59%Pogona vitticeps	–	–

Genera of Agamidae

GC content of the whole genome, % of A + C + G + T

Region

Parameter

Chart

Genera of Agamidae

Calotes	1	40.26%	–	–	40.26%Calotes versicolor	40.26%	40.26%Calotes versicolor	–	–
Chlamydosaurus	1	41.44%	–	–	41.44%Chlamydosaurus kingii	41.44%	41.44%Chlamydosaurus kingii	–	–
Hydrosaurus	1	41.82%	–	–	41.82%Hydrosaurus amboinensis	41.82%	41.82%Hydrosaurus amboinensis	–	–
Pogona	1	43.04%	–	–	43.04%Pogona vitticeps	43.04%	43.04%Pogona vitticeps	–	–

Codon usage

Share of each codon in all 13 protein-coding genes, across Agamidae

Gene

Loading codon usage…

Every species, region by region

Each region's page lists the value of every species, with the same statistics by class, order or family and a CSV download.

Whole genome Protein-coding All rRNA All tRNA 12S rRNA 16S rRNA D-loop ND1 ND2 COX1 COX2 ATP8 ATP6 COX3 ND3 ND4L ND4 ND5 ND6 CYTB

Agamidae taxon page All data downloads

The charts

Each chart draws the rows of the table under it, in the table's order: sort a column to reorder the chart.Chart sets its axis.
Distribution: the range (line), mean ± SD (bar), median (tick) and mean (dot). Lengths of the regions are on a log scale.
Variation: the coefficient of variation, or the SD for the skews, which vary around zero.
Lifespan r: r with its 95% confidence interval (Fisher z). Lifespan map: r of every parameter in every region at once, bold where the Benjamini–Hochberg q-value over the map is below 0.05.

What the numbers are

Species: species with the region annotated. SD is the sample standard deviation, CV = SD / mean.
Base percentages are over A + C + G + T, so GC % + AT % = 100. Skews are on the L strand as deposited in RefSeq: GC skew = (G − C) / (G + C), AT skew = (A − T) / (A + T).
Min and Max name the species with the extreme value.

Lifespan columns

r is the Pearson correlation of the parameter with log₁₀ maximum lifespan within the group (5 or more species), and p its two-tailed p-value, as on the original MitoAge. They are not corrected for multiple testing or for shared ancestry: the plot shows Benjamini–Hochberg q-values and phylogenetic contrasts.

The original site labelled the base columns with their complements, so its skews have the opposite sign. Seemethods.