family · mtDNA statistics

Salmonidae

36 species in 10 genera. Every region of their mitochondrial genomes, side by side.

Group

species

46.0%

mean GC, whole genome

SD 1.0, range 44.3–47.6%

16,662

median genome length, bp

Range 16,526–16,864 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	36	46.03%	1.03	0.022	44.30%Thymallus arcticus	45.84%	47.59%Coregonus clupeaformis	0.22	0.2
Protein-coding	36	46.06%	1.30	0.028	43.96%Oncorhynchus masou	45.71%	48.05%Coregonus clupeaformis	0.24	0.16
All rRNA	36	48.91%	0.39	0.008	48.15%Oncorhynchus masou	48.85%	49.51%Coregonus nasus	0.37	0.03
All tRNA	36	45.65%	0.57	0.013	44.63%Salvelinus leucomaenis	45.67%	46.82%Prosopium williamsoni	−0.02	0.91
12S rRNA	36	50.23%	0.28	0.005	49.68%Salmo salar	50.26%	51.00%Prosopium cylindraceum	0.25	0.15
16S rRNA	36	48.17%	0.53	0.011	47.23%Oncorhynchus masou	48.00%	48.96%Stenodus leucichthys	0.35	0.03
D-loop	36	38.13%	1.64	0.043	34.13%Thymallus arcticus	38.56%	41.11%Prosopium cylindraceum	−0.08	0.64
ND1	36	47.26%	1.53	0.032	44.86%Brachymystax lenok	47.13%	50.26%Prosopium williamsoni	0.12	0.49
ND2	36	45.98%	1.93	0.042	42.99%Thymallus arcticus	45.48%	49.24%Coregonus lavaretus	0.28	0.1
COX1	36	45.77%	1.17	0.026	43.20%Oncorhynchus masou	45.58%	47.90%Coregonus autumnalis	0.32	0.06
COX2	36	44.74%	0.76	0.017	43.27%Oncorhynchus masou	44.86%	46.17%Salvelinus namaycush	0.45	0.006
ATP8	36	46.38%	1.74	0.037	43.45%Salvelinus alpinus	46.43%	48.81%Coregonus nasus	0.05	0.77
ATP6	36	45.50%	1.71	0.038	41.96%Thymallus thymallus	45.83%	47.81%Coregonus clupeaformis	0.30	0.08
COX3	36	46.97%	1.29	0.027	44.27%Oncorhynchus masou	46.75%	49.17%Coregonus nasus	0.06	0.71
ND3	36	47.49%	2.02	0.042	42.98%Thymallus thymallus	47.85%	50.43%Salvelinus malma	0.43	0.009
ND4L	36	49.89%	1.62	0.033	46.80%Thymallus arcticus	49.49%	53.54%Coregonus artedi	0.14	0.41
ND4	36	44.97%	1.57	0.035	41.85%Thymallus arcticus	44.79%	47.36%Coregonus autumnalis	0.10	0.57
ND5	36	44.49%	1.71	0.039	42.52%Salvelinus fontinalis	43.94%	47.42%Coregonus clupeaformis	0.17	0.32
ND6	36	48.97%	1.68	0.034	46.36%Salmo salar	48.37%	51.92%Coregonus ussuriensis	0.17	0.32
CYTB	36	46.62%	1.16	0.025	44.26%Thymallus nigrescens	46.71%	48.20%Coregonus nasus	0.22	0.2

Genera of Salmonidae

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

Region

Parameter

Chart

Genera of Salmonidae

Coregonus	9	47.43%	0.24	0.005	47.00%Coregonus hoyi	47.55%	47.59%Coregonus clupeaformis	0.50	0.17
Oncorhynchus	8	45.76%	0.54	0.012	44.55%Oncorhynchus masou	45.86%	46.25%Oncorhynchus kisutch	0.53	0.18
Salvelinus	5	45.51%	0.30	0.007	45.21%Salvelinus fontinalis	45.47%	45.97%Salvelinus namaycush	0.64	0.24
Thymallus	5	44.69%	0.32	0.007	44.30%Thymallus arcticus	44.59%	45.14%Thymallus tugarinae	−0.85	0.07
Hucho	2	45.44%	0.09	0.002	45.38%Hucho taimen	45.44%	45.50%Hucho hucho	–	–
Prosopium	2	46.70%	0.38	0.008	46.44%Prosopium cylindraceum	46.70%	46.97%Prosopium williamsoni	–	–
Salmo	2	45.57%	0.49	0.011	45.23%Salmo salar	45.57%	45.92%Salmo trutta	–	–
Stenodus	1	47.20%	–	–	47.20%Stenodus leucichthys	47.20%	47.20%Stenodus leucichthys	–	–
Parahucho	1	45.30%	–	–	45.30%Parahucho perryi	45.30%	45.30%Parahucho perryi	–	–
Brachymystax	1	45.17%	–	–	45.17%Brachymystax lenok	45.17%	45.17%Brachymystax lenok	–	–

Codon usage

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

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

Salmonidae 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.