class · mtDNA statistics

Actinopterygii

Ray-finned fishes: 895 species in 62 orders. Every region of their mitochondrial genomes, side by side.

Group

895

species

45.3%

mean GC, whole genome

SD 2.1, range 36.8–51.4%

16,611

median genome length, bp

Range 12,946–19,801 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	895	45.27%	2.12	0.047	36.82%Conger myriaster	45.47%	51.41%Trachinocephalus myops	0.02	0.48
Protein-coding	895	45.75%	2.44	0.053	36.93%Erpetoichthys calabaricus	46.03%	52.02%Centrolabrus exoletus	0.05	0.11
All rRNA	894	46.51%	1.68	0.036	38.09%Nothobranchius kuhntae	46.69%	52.08%Trachinocephalus myops	0.08	0.02
All tRNA	895	45.12%	1.47	0.033	38.15%Nothobranchius kuhntae	45.34%	52.41%Trachinocephalus myops	−0.06	0.08
12S rRNA	894	48.51%	1.70	0.035	40.53%Nothobranchius kuhntae	48.64%	54.28%Trachinocephalus myops	0.09	0.01
16S rRNA	893	45.38%	1.92	0.042	36.71%Nothobranchius kuhntae	45.64%	50.92%Tenualosa toli	0.07	0.04
D-loop	772	36.00%	8.03	0.223	0.00%Coryphaena equiselis	36.72%	100.00%Polyprion americanus	−0.08	0.02
ND1	895	46.77%	2.76	0.059	36.31%Spinachia spinachia	47.08%	54.87%Trachinocephalus myops	0.03	0.3
ND2	895	47.12%	3.21	0.068	34.55%Conger myriaster	47.56%	55.31%Centrolabrus exoletus	−0.02	0.6
COX1	895	45.42%	2.16	0.048	37.65%Aphyosemion australe	45.57%	51.77%Neosalanx taihuensis	0.08	0.02
COX2	895	43.77%	2.09	0.048	36.61%Fundulus heteroclitus	43.85%	51.09%Diaphus theta	0.04	0.29
ATP8	895	43.32%	3.98	0.092	30.36%Betta splendens	43.45%	54.76%Parupeneus heptacantha	0.17	4.7 × 10⁻⁷
ATP6	895	44.59%	3.13	0.070	34.50%Betta splendens	44.88%	52.27%Monotaxis grandoculis	0.09	0.005
COX3	895	46.97%	2.26	0.048	38.85%Nothobranchius kuhntae	47.01%	52.36%Parupeneus heptacantha	0.01	0.75
ND3	895	46.82%	3.45	0.074	33.33%Spinachia spinachia	47.29%	55.68%Centrolabrus exoletus	0.16	1.9 × 10⁻⁶
ND4L	895	48.71%	3.01	0.062	37.37%Conger myriaster	48.82%	57.24%Diaphus theta	0.09	0.01
ND4	895	45.63%	2.89	0.063	35.19%Spinachia spinachia	46.04%	53.22%Rhinogobius cliffordpopei	0.06	0.09
ND5	895	44.42%	2.69	0.061	33.55%Erpetoichthys calabaricus	44.75%	52.50%Centrolabrus exoletus	0.05	0.11
ND6	894	46.77%	3.11	0.067	35.07%Nothobranchius kuhntae	46.83%	59.20%Trachinocephalus myops	0.01	0.85
CYTB	895	45.81%	2.56	0.056	36.20%Erpetoichthys calabaricus	46.01%	51.80%Dissostichus eleginoides	0.03	0.43

Orders of Actinopterygii

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

Region

Parameter

Chart

Orders of Actinopterygii

Perciformes	220	45.59%	1.52	0.033	38.09%Betta splendens	45.61%	49.21%Zoarces viviparus	−0.10	0.15
Cypriniformes	136	43.91%	1.27	0.029	39.93%Danio rerio	43.96%	46.51%Notropis buccata	0.05	0.58
Clupeiformes	42	46.93%	1.84	0.039	42.36%Coilia mystus	47.25%	50.07%Sardina pilchardus	0.06	0.72
Salmoniformes	36	46.03%	1.03	0.022	44.30%Thymallus arcticus	45.84%	47.59%Coregonus clupeaformis	0.22	0.2
Pleuronectiformes	35	45.58%	1.69	0.037	39.59%Cynoglossus joyneri	46.06%	47.22%Pseudorhombus pentophthalmus	0.26	0.14
Siluriformes	25	43.52%	1.16	0.027	41.20%Bagrus docmak	43.77%	45.26%Ictalurus furcatus	0.42	0.04
Centrarchiformes	24	45.52%	2.00	0.044	38.44%Elassoma alabamae	45.91%	48.16%Lepomis megalotis	0.43	0.04
Scombriformes	24	45.82%	1.52	0.033	40.83%Pampus argenteus	46.14%	47.71%Rastrelliger kanagurta	0.17	0.43
Spariformes	22	45.38%	1.36	0.030	42.67%Nemipterus bathybius	45.50%	48.75%Monotaxis grandoculis	0.19	0.39
Carangiformes	22	46.04%	1.55	0.034	41.13%Coryphaena equiselis	46.36%	47.99%Seriola lalandi	0.22	0.32
Acipenseriformes	21	45.75%	0.36	0.008	45.34%Acipenser baerii	45.63%	46.63%Scaphirhynchus albus	0.09	0.69
Gadiformes	20	43.74%	2.03	0.046	41.01%Melanogrammus aeglefinus	43.07%	48.32%Merluccius merluccius	−0.12	0.6
Cyprinodontiformes	17	42.59%	3.19	0.075	37.77%Aphyosemion australe	42.99%	47.82%Xiphophorus hellerii	0.18	0.5
Gobiiformes	16	46.32%	2.47	0.053	40.40%Perccottus glenii	46.31%	49.93%Eviota epiphanes	−0.41	0.12
Lutjaniformes	16	46.97%	0.51	0.011	45.91%Lutjanus erythropterus	47.14%	47.81%Diagramma pictum	0.02	0.94

Codon usage

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

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

Actinopterygii 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.