order · mtDNA statistics

Scombriformes

24 species in 7 families. Every region of their mitochondrial genomes, side by side.

Group

species

45.8%

mean GC, whole genome

SD 1.5, range 40.8–47.7%

16,544

median genome length, bp

Range 16,406–17,098 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	24	45.82%	1.52	0.033	40.83%Pampus argenteus	46.14%	47.71%Rastrelliger kanagurta	0.17	0.43
Protein-coding	24	46.52%	1.73	0.037	41.08%Pampus argenteus	46.82%	48.74%Rastrelliger kanagurta	0.17	0.44
All rRNA	24	46.62%	0.89	0.019	43.68%Pampus argenteus	46.94%	48.03%Scomberomorus munroi	0.25	0.25
All tRNA	24	45.13%	1.13	0.025	41.62%Pampus argenteus	45.44%	46.39%Taractichthys steindachneri	0.08	0.72
12S rRNA	24	48.42%	1.22	0.025	44.34%Pampus argenteus	48.79%	49.79%Scomberomorus munroi	0.25	0.24
16S rRNA	24	45.62%	0.89	0.019	43.31%Pampus argenteus	45.79%	47.53%Trichiurus japonicus	0.19	0.37
D-loop	22	36.38%	2.40	0.066	29.33%Tentoriceps cristatus	37.44%	38.51%Euthynnus alletteratus	0.13	0.57
ND1	24	47.46%	1.73	0.036	42.87%Pampus argenteus	47.64%	50.05%Aphanopus carbo	0.16	0.45
ND2	24	48.15%	2.09	0.043	41.78%Pampus argenteus	48.54%	51.53%Aphanopus carbo	0.34	0.11
COX1	24	46.13%	1.60	0.035	41.18%Pampus argenteus	46.16%	48.64%Rastrelliger kanagurta	0.08	0.71
COX2	24	44.23%	1.37	0.031	40.23%Pampus argenteus	44.43%	46.31%Scomber colias	0.30	0.15
ATP8	24	45.14%	3.46	0.077	38.10%Pampus argenteus	45.35%	50.00%Rastrelliger kanagurta	−0.07	0.75
ATP6	24	45.17%	2.16	0.048	38.30%Pampus argenteus	45.25%	49.05%Aphanopus carbo	0.15	0.49
COX3	24	47.44%	1.76	0.037	43.31%Pampus argenteus	47.80%	50.25%Rastrelliger kanagurta	0.13	0.53
ND3	24	49.29%	2.84	0.058	41.55%Pampus argenteus	50.21%	52.57%Rastrelliger brachysoma	0.18	0.39
ND4L	24	49.49%	2.69	0.054	43.77%Pampus argenteus	50.34%	52.86%Rastrelliger brachysoma	0.06	0.78
ND4	24	46.33%	2.12	0.046	41.42%Pampus argenteus	46.34%	50.47%Rastrelliger kanagurta	0.08	0.71
ND5	24	45.57%	1.97	0.043	39.86%Pampus argenteus	46.00%	48.40%Aphanopus carbo	0.20	0.35
ND6	24	45.93%	2.86	0.062	38.12%Pampus argenteus	46.26%	52.11%Taractichthys steindachneri	0.08	0.72
CYTB	24	46.49%	1.65	0.035	41.78%Pampus argenteus	46.93%	48.55%Auxis rochei	0.06	0.77

Families of Scombriformes

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

Region

Parameter

Chart

Families of Scombriformes

Scombridae	14	46.43%	0.71	0.015	45.03%Scomberomorus semifasciatus	46.43%	47.71%Rastrelliger kanagurta	−0.60	0.02
Trichiuridae	3	45.82%	1.65	0.036	44.30%Tentoriceps cristatus	45.58%	47.57%Aphanopus carbo	–	–
Gempylidae	2	45.75%	0.14	0.003	45.65%Promethichthys prometheus	45.75%	45.85%Thyrsites atun	–	–
Bramidae	2	45.65%	2.45	0.054	43.92%Pteraclis aesticola	45.65%	47.38%Taractichthys steindachneri	–	–
Centrolophidae	1	44.10%	–	–	44.10%Psenopsis anomala	44.10%	44.10%Psenopsis anomala	–	–
Stromateidae	1	40.83%	–	–	40.83%Pampus argenteus	40.83%	40.83%Pampus argenteus	–	–
Nomeidae	1	44.35%	–	–	44.35%Cubiceps pauciradiatus	44.35%	44.35%Cubiceps pauciradiatus	–	–

Codon usage

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

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

Scombriformes 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.