family · mtDNA statistics

Alligatoridae

5 species in 3 genera. Every region of their mitochondrial genomes, side by side.

Group

species

45.3%

mean GC, whole genome

SD 2.4, range 42.5–47.6%

16,646

median genome length, bp

Range 14,935–17,900 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	5	45.31%	2.39	0.053	42.55%Caiman crocodilus	45.98%	47.60%Paleosuchus palpebrosus	−0.53	0.36
Protein-coding	5	46.06%	2.02	0.044	43.48%Alligator mississippiensis	46.63%	47.92%Paleosuchus trigonatus	−0.63	0.26
All rRNA	5	45.93%	1.12	0.024	44.35%Alligator mississippiensis	46.06%	46.96%Paleosuchus palpebrosus	−0.51	0.38
All tRNA	5	44.28%	0.83	0.019	43.23%Alligator mississippiensis	44.01%	45.37%Paleosuchus palpebrosus	−0.64	0.25
12S rRNA	5	48.38%	1.04	0.021	46.73%Paleosuchus trigonatus	48.68%	49.24%Alligator sinensis	−0.11	0.86
16S rRNA	5	44.55%	1.80	0.040	42.08%Alligator mississippiensis	45.54%	46.25%Paleosuchus palpebrosus	−0.61	0.28
D-loop	3	37.27%	11.75	0.315	28.41%Caiman crocodilus	32.79%	50.59%Paleosuchus trigonatus	–	–
ND1	5	46.54%	2.60	0.056	43.48%Caiman crocodilus	47.00%	49.59%Paleosuchus palpebrosus	−0.58	0.3
ND2	5	44.02%	2.77	0.063	39.74%Alligator mississippiensis	45.07%	46.55%Paleosuchus palpebrosus	−0.71	0.18
COX1	5	46.13%	1.53	0.033	44.44%Alligator mississippiensis	46.99%	47.46%Paleosuchus trigonatus	−0.35	0.56
COX2	5	45.20%	2.02	0.045	42.59%Caiman crocodilus	46.51%	46.80%Alligator sinensis	−0.30	0.63
ATP8	5	45.13%	3.73	0.083	40.83%Caiman crocodilus	46.99%	48.52%Paleosuchus palpebrosus	−0.48	0.41
ATP6	5	44.96%	1.58	0.035	43.51%Alligator mississippiensis	45.18%	47.37%Paleosuchus trigonatus	−0.33	0.59
COX3	5	48.44%	1.77	0.037	46.17%Alligator mississippiensis	48.85%	50.26%Paleosuchus trigonatus	−0.62	0.27
ND3	5	44.66%	1.11	0.025	43.39%Caiman crocodilus	44.54%	46.26%Alligator sinensis	0.19	0.76
ND4L	5	47.26%	3.02	0.064	44.56%Alligator mississippiensis	45.92%	50.68%Paleosuchus trigonatus	−0.82	0.09
ND4	5	46.44%	2.01	0.043	43.30%Alligator mississippiensis	46.87%	48.80%Paleosuchus palpebrosus	−0.93	0.02
ND5	5	45.03%	2.14	0.048	42.55%Alligator mississippiensis	46.07%	47.15%Paleosuchus trigonatus	−0.37	0.54
ND6	5	47.33%	2.72	0.057	44.19%Alligator mississippiensis	46.12%	50.19%Paleosuchus palpebrosus	−0.82	0.09
CYTB	5	47.44%	2.90	0.061	44.09%Alligator mississippiensis	47.28%	50.48%Paleosuchus trigonatus	−0.69	0.19

Genera of Alligatoridae

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

Region

Parameter

Chart

Genera of Alligatoridae

Alligator	2	44.50%	2.08	0.047	43.03%Alligator mississippiensis	44.50%	45.98%Alligator sinensis	–	–
Paleosuchus	2	47.50%	0.15	0.003	47.39%Paleosuchus trigonatus	47.50%	47.60%Paleosuchus palpebrosus	–	–
Caiman	1	42.55%	–	–	42.55%Caiman crocodilus	42.55%	42.55%Caiman crocodilus	–	–

Codon usage

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

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

Alligatoridae 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.