family · mtDNA statistics

Cottidae

24 species in 8 genera. Every region of their mitochondrial genomes, side by side.

Group

species

47.0%

mean GC, whole genome

SD 0.8, range 45.7–48.6%

16,565

median genome length, bp

Range 16,384–16,959 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	24	47.03%	0.76	0.016	45.68%Cottus klamathensis	47.04%	48.57%Alpinocottus poecilopus	0.15	0.47
Protein-coding	24	47.94%	1.10	0.023	45.95%Cottus klamathensis	47.91%	49.63%Triglops forficatus	0.30	0.15
All rRNA	24	47.01%	0.46	0.010	46.12%Cottus pitensis	46.95%	47.73%Hemilepidotus gilberti	0.17	0.42
All tRNA	24	46.07%	0.49	0.011	45.35%Cottus pitensis	46.04%	47.55%Cottus pollux	−0.26	0.23
12S rRNA	24	48.24%	0.51	0.011	47.42%Cottus klamathensis	48.23%	49.05%Hemilepidotus gilberti	0.25	0.23
16S rRNA	24	46.32%	0.55	0.012	45.32%Cottus pitensis	46.32%	47.15%Cottus pollux	0.10	0.66
D-loop	17	38.23%	2.57	0.067	33.19%Gymnocanthus tricuspis	38.51%	44.34%Cottus klamathensis	−0.56	0.02
ND1	24	49.21%	1.51	0.031	46.05%Myoxocephalus scorpius	49.33%	52.10%Alpinocottus poecilopus	0.04	0.86
ND2	24	48.78%	1.37	0.028	46.03%Cottus cognatus	48.97%	51.63%Alpinocottus poecilopus	0.11	0.6
COX1	24	47.51%	0.85	0.018	46.23%Cottus confusus	47.28%	48.87%Gymnocanthus pistilliger	0.33	0.12
COX2	24	45.84%	0.67	0.015	44.43%Myoxocephalus quadricornis	45.88%	47.32%Alpinocottus poecilopus	−0.45	0.03
ATP8	24	47.79%	1.80	0.038	45.24%Cottus pitensis	47.62%	51.19%Gymnocanthus tricuspis	0.06	0.79
ATP6	24	48.68%	1.62	0.033	45.61%Cottus klamathensis	48.68%	51.90%Hemilepidotus gilberti	0.20	0.36
COX3	24	48.34%	1.05	0.022	46.37%Cottus klamathensis	48.31%	49.94%Alpinocottus poecilopus	0.31	0.13
ND3	24	50.05%	2.67	0.053	45.85%Cottus pitensis	49.57%	54.15%Gymnocanthus detrisus	0.21	0.32
ND4L	24	50.79%	1.19	0.023	48.15%Cottus confusus	50.67%	53.20%Icelus spatula	−0.14	0.5
ND4	24	47.55%	1.39	0.029	44.53%Cottus klamathensis	47.79%	50.54%Alpinocottus poecilopus	0.10	0.63
ND5	24	46.19%	1.56	0.034	43.83%Cottus klamathensis	46.28%	48.50%Triglops forficatus	0.45	0.03
ND6	24	48.21%	2.65	0.055	44.44%Cottus klamathensis	47.89%	54.02%Gymnocanthus pistilliger	0.34	0.11
CYTB	24	48.63%	1.17	0.024	46.36%Cottus pollux	48.51%	51.01%Gymnocanthus pistilliger	0.55	0.006

Genera of Cottidae

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

Region

Parameter

Chart

Genera of Cottidae

Cottus	9	46.50%	0.56	0.012	45.68%Cottus klamathensis	46.50%	47.54%Cottus pollux	−0.13	0.74
Gymnocanthus	4	47.69%	0.34	0.007	47.50%Gymnocanthus herzensteini	47.53%	48.20%Gymnocanthus pistilliger	–	–
Myoxocephalus	3	46.36%	0.37	0.008	46.01%Myoxocephalus scorpius	46.32%	46.75%Myoxocephalus quadricornis	–	–
Triglops	3	47.50%	0.66	0.014	46.75%Triglops scepticus	47.74%	48.01%Triglops forficatus	–	–
Hemilepidotus	2	47.33%	0.12	0.002	47.25%Hemilepidotus jordani	47.33%	47.41%Hemilepidotus gilberti	–	–
Alpinocottus	1	48.57%	–	–	48.57%Alpinocottus poecilopus	48.57%	48.57%Alpinocottus poecilopus	–	–
Comephorus	1	47.19%	–	–	47.19%Comephorus baikalensis	47.19%	47.19%Comephorus baikalensis	–	–
Icelus	1	47.51%	–	–	47.51%Icelus spatula	47.51%	47.51%Icelus spatula	–	–

Codon usage

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

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

Cottidae 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.