family · mtDNA statistics

Scombridae

24 species in 9 genera. Every region of their mitochondrial genomes, side by side.

Group

species

46.5%

mean GC, whole genome

SD 0.6, range 45.0–47.7%

16,528

median genome length, bp

Range 16,501–16,796 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	24	46.50%	0.62	0.013	45.03%Scomberomorus semifasciatus	46.43%	47.71%Rastrelliger kanagurta	−0.41	0.04
Protein-coding	24	47.21%	0.80	0.017	45.37%Scomberomorus semifasciatus	47.01%	48.74%Rastrelliger kanagurta	−0.42	0.04
All rRNA	24	46.97%	0.32	0.007	46.43%Scomberomorus sierra	46.99%	48.03%Scomberomorus munroi	−0.12	0.59
All tRNA	24	45.63%	0.28	0.006	45.03%Scomberomorus semifasciatus	45.60%	46.19%Rastrelliger kanagurta	−0.14	0.52
12S rRNA	24	48.94%	0.46	0.009	47.71%Scomber colias	49.05%	49.79%Scomberomorus munroi	−0.16	0.47
16S rRNA	24	45.91%	0.45	0.010	44.98%Scomberomorus sierra	45.81%	47.03%Scomberomorus munroi	0.01	0.95
D-loop	22	37.77%	0.70	0.018	36.25%Sarda sarda	37.82%	38.87%Euthynnus affinis	−0.06	0.79
ND1	24	48.03%	1.03	0.022	45.74%Scomberomorus semifasciatus	47.92%	50.05%Scomber japonicus	−0.22	0.31
ND2	24	49.24%	1.01	0.020	46.56%Scomberomorus semifasciatus	49.64%	50.57%Scomber japonicus	0.26	0.22
COX1	24	46.59%	1.02	0.022	45.32%Scomberomorus semifasciatus	46.20%	48.72%Scomber japonicus	−0.32	0.13
COX2	24	44.91%	0.95	0.021	43.42%Scomberomorus semifasciatus	44.57%	47.47%Scomber scombrus	0.32	0.12
ATP8	24	46.60%	1.89	0.040	42.26%Scomberomorus semifasciatus	46.43%	50.00%Rastrelliger kanagurta	−0.54	0.007
ATP6	24	45.37%	1.15	0.025	43.86%Thunnus alalunga	45.25%	47.37%Auxis thazard	−0.66	4.9 × 10⁻⁴
COX3	24	47.60%	1.09	0.023	46.11%Thunnus tonggol	47.64%	50.25%Rastrelliger kanagurta	−0.44	0.03
ND3	24	50.79%	1.48	0.029	45.85%Scomberomorus semifasciatus	51.29%	52.57%Rastrelliger brachysoma	−0.05	0.81
ND4L	24	50.70%	1.82	0.036	46.80%Thunnus thynnus	51.18%	53.87%Auxis thazard	−0.43	0.04
ND4	24	47.24%	1.40	0.030	44.39%Scomberomorus semifasciatus	47.07%	50.47%Rastrelliger kanagurta	−0.45	0.03
ND5	24	46.38%	0.93	0.020	44.32%Scomberomorus semifasciatus	46.30%	47.85%Katsuwonus pelamis	−0.33	0.11
ND6	24	46.10%	1.73	0.038	42.15%Scomberomorus semifasciatus	46.26%	49.43%Scomberomorus munroi	−0.58	0.003
CYTB	24	47.25%	0.84	0.018	45.84%Sarda sarda	47.28%	48.55%Scomber scombrus	−0.32	0.12

Genera of Scombridae

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

Region

Parameter

Chart

Genera of Scombridae

Thunnus	8	46.16%	0.06	0.001	46.11%Thunnus thynnus	46.14%	46.25%Thunnus maccoyii	−0.02	0.97
Scomberomorus	4	45.93%	0.67	0.015	45.03%Scomberomorus semifasciatus	46.10%	46.49%Scomberomorus cavalla	–	–
Scomber	3	46.97%	0.03	0.001	46.94%Scomber scombrus	46.98%	46.99%Scomber japonicus	–	–
Auxis	2	47.14%	0.15	0.003	47.03%Auxis rochei	47.14%	47.24%Auxis thazard	–	–
Euthynnus	2	46.81%	0.44	0.009	46.50%Euthynnus alletteratus	46.81%	47.12%Euthynnus affinis	–	–
Rastrelliger	2	47.59%	0.16	0.003	47.48%Rastrelliger brachysoma	47.59%	47.71%Rastrelliger kanagurta	–	–
Katsuwonus	1	46.89%	–	–	46.89%Katsuwonus pelamis	46.89%	46.89%Katsuwonus pelamis	–	–
Sarda	1	45.71%	–	–	45.71%Sarda sarda	45.71%	45.71%Sarda sarda	–	–
Acanthocybium	1	46.45%	–	–	46.45%Acanthocybium solandri	46.45%	46.45%Acanthocybium solandri	–	–

Codon usage

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

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

Scombridae 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.