class · mtDNA statistics

Amphibia

Amphibians: 47 species in 3 orders. Every region of their mitochondrial genomes, side by side.

Group

species

38.2%

mean GC, whole genome

SD 3.5, range 31.6–44.0%

16,730

median genome length, bp

Range 16,061–24,317 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	47	38.16%	3.50	0.092	31.62%Dermophis mexicanus	37.92%	44.01%Pipa pipa	0.03	0.82
Protein-coding	47	38.48%	4.09	0.106	31.05%Onychodactylus fischeri	38.21%	45.97%Pipa pipa	0.04	0.82
All rRNA	47	38.69%	3.44	0.089	33.15%Onychodactylus fischeri	39.10%	45.72%Pipa pipa	0.03	0.85
All tRNA	47	38.81%	3.83	0.099	31.42%Dermophis mexicanus	38.53%	44.55%Bombina variegata	0.02	0.91
12S rRNA	47	41.84%	3.60	0.086	35.52%Dermophis mexicanus	42.76%	48.03%Pipa pipa	0.05	0.76
16S rRNA	47	36.84%	3.49	0.095	31.00%Afghanodon mustersi	36.56%	44.40%Pipa pipa	0.02	0.89
D-loop	44	34.87%	2.47	0.071	27.32%Xenopus laevis	34.91%	38.38%Microhyla ornata	−0.12	0.45
ND1	47	37.82%	4.20	0.111	30.74%Dermophis mexicanus	37.67%	46.58%Pipa pipa	0.02	0.87
ND2	47	36.39%	5.01	0.138	27.86%Onychodactylus fischeri	37.17%	44.02%Bombina orientalis	0.07	0.63
COX1	47	40.86%	3.54	0.087	33.72%Onychodactylus fischeri	40.97%	47.39%Pipa pipa	0.04	0.79
COX2	47	38.70%	3.43	0.089	31.88%Onychodactylus fischeri	39.10%	45.26%Pipa pipa	0.02	0.91
ATP8	47	32.28%	4.94	0.153	24.40%Ambystoma tigrinum	32.73%	44.64%Pipa pipa	−0.02	0.88
ATP6	47	37.46%	4.41	0.118	29.09%Onychodactylus fischeri	37.83%	46.93%Pipa pipa	0.06	0.67
COX3	47	41.54%	3.85	0.093	34.95%Dermophis mexicanus	41.20%	47.96%Pelophylax nigromaculatus	−0.02	0.88
ND3	47	38.88%	4.73	0.122	28.49%Onychodactylus fischeri	39.08%	47.23%Pipa pipa	0.03	0.85
ND4L	47	38.77%	5.32	0.137	31.31%Ambystoma mexicanum	37.71%	50.17%Bombina variegata	0.13	0.4
ND4	47	37.84%	4.37	0.116	29.83%Onychodactylus fischeri	37.66%	45.50%Pipa pipa	0.06	0.68
ND5	47	36.46%	4.26	0.117	28.45%Dermophis mexicanus	35.49%	45.25%Pipa pipa	0.01	0.94
ND6	47	39.53%	4.73	0.120	30.81%Ambystoma texanum	40.46%	47.90%Pelophylax nigromaculatus	−0.02	0.88
CYTB	47	39.98%	4.34	0.108	31.99%Onychodactylus fischeri	40.89%	47.86%Pelophylax nigromaculatus	0.00	0.99

Orders of Amphibia

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

Region

Parameter

Chart

Orders of Amphibia

Caudata	27	36.43%	2.90	0.080	31.66%Onychodactylus fischeri	36.16%	41.83%Proteus anguinus	0.22	0.28
Anura	19	40.95%	2.02	0.049	36.99%Xenopus laevis	40.95%	44.01%Pipa pipa	−0.06	0.81
Gymnophiona	1	31.62%	–	–	31.62%Dermophis mexicanus	31.62%	31.62%Dermophis mexicanus	–	–

Codon usage

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

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

Amphibia taxon page Plot GC content against GC skew 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.