family · mtDNA statistics

Pomacentridae

4 species in 2 genera. Every region of their mitochondrial genomes, side by side.

Group

species

45.1%

mean GC, whole genome

SD 0.4, range 44.7–45.5%

16,768

median genome length, bp

Range 16,649–16,976 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	4	45.07%	0.40	0.009	44.70%Amphiprion clarkii	45.06%	45.47%Abudefduf saxatilis	–	–
Protein-coding	4	45.73%	0.44	0.010	45.25%Amphiprion clarkii	45.78%	46.14%Abudefduf saxatilis	–	–
All rRNA	4	46.11%	0.15	0.003	45.90%Amphiprion clarkii	46.15%	46.24%Amphiprion ocellaris	–	–
All tRNA	4	45.06%	0.76	0.017	44.07%Amphiprion ephippium	45.16%	45.85%Abudefduf saxatilis	–	–
12S rRNA	4	48.20%	0.36	0.008	47.73%Abudefduf saxatilis	48.28%	48.52%Amphiprion ocellaris	–	–
16S rRNA	4	44.90%	0.33	0.007	44.64%Amphiprion ephippium	44.81%	45.35%Abudefduf saxatilis	–	–
D-loop	4	34.38%	1.21	0.035	32.79%Amphiprion ephippium	34.56%	35.58%Amphiprion clarkii	–	–
ND1	4	45.85%	0.56	0.012	45.13%Amphiprion ephippium	45.90%	46.46%Abudefduf saxatilis	–	–
ND2	4	46.46%	0.63	0.014	45.74%Amphiprion clarkii	46.41%	47.27%Amphiprion ocellaris	–	–
COX1	4	45.12%	0.12	0.003	44.99%Abudefduf saxatilis	45.10%	45.27%Amphiprion clarkii	–	–
COX2	4	44.21%	0.68	0.015	43.70%Amphiprion clarkii	43.99%	45.15%Abudefduf saxatilis	–	–
ATP8	4	44.20%	2.14	0.048	42.26%Amphiprion ocellaris	43.75%	47.02%Abudefduf saxatilis	–	–
ATP6	4	44.53%	2.02	0.045	42.17%Amphiprion ephippium	44.62%	46.71%Amphiprion ocellaris	–	–
COX3	4	47.83%	0.57	0.012	47.13%Abudefduf saxatilis	47.83%	48.54%Amphiprion ocellaris	–	–
ND3	4	46.99%	0.41	0.009	46.70%Amphiprion ocellaris	46.85%	47.56%Abudefduf saxatilis	–	–
ND4L	4	49.49%	0.55	0.011	48.82%Amphiprion clarkii	49.49%	50.17%Amphiprion ocellaris	–	–
ND4	4	46.83%	0.91	0.019	45.98%Abudefduf saxatilis	46.71%	47.94%Amphiprion ocellaris	–	–
ND5	4	44.52%	1.01	0.023	43.55%Amphiprion clarkii	44.28%	45.95%Abudefduf saxatilis	–	–
ND6	4	45.69%	0.96	0.021	44.64%Amphiprion clarkii	45.59%	46.93%Amphiprion ocellaris	–	–
CYTB	4	45.33%	0.67	0.015	44.79%Amphiprion ocellaris	45.14%	46.28%Abudefduf saxatilis	–	–

Genera of Pomacentridae

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

Region

Parameter

Chart

Genera of Pomacentridae

Amphiprion	3	44.94%	0.37	0.008	44.70%Amphiprion clarkii	44.76%	45.37%Amphiprion ocellaris	–	–
Abudefduf	1	45.47%	–	–	45.47%Abudefduf saxatilis	45.47%	45.47%Abudefduf saxatilis	–	–

Codon usage

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

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

Pomacentridae 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.