family · mtDNA statistics

Clupeidae

30 species in 18 genera. Every region of their mitochondrial genomes, side by side.

Group

species

47.8%

mean GC, whole genome

SD 1.2, range 45.3–50.1%

16,694

median genome length, bp

Range 16,541–17,158 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	30	47.76%	1.17	0.024	45.29%Potamalosa richmondia	47.70%	50.07%Sardina pilchardus	−0.18	0.34
Protein-coding	30	48.12%	1.36	0.028	45.09%Potamalosa richmondia	48.16%	50.82%Escualosa thoracata	−0.15	0.43
All rRNA	30	49.29%	0.72	0.015	48.22%Clupea harengus	49.35%	51.08%Tenualosa toli	−0.46	0.01
All tRNA	30	48.04%	0.67	0.014	46.73%Sardinella longiceps	47.89%	49.48%Sardina pilchardus	0.04	0.83
12S rRNA	30	50.70%	0.48	0.009	49.38%Escualosa thoracata	50.76%	51.37%Dorosoma cepedianum	−0.31	0.1
16S rRNA	30	48.49%	1.03	0.021	46.84%Amblygaster sirm	48.44%	50.92%Tenualosa toli	−0.42	0.02
D-loop	28	37.89%	8.24	0.217	0.00%Sardinella aurita	38.20%	49.53%Sardinella lemuru	−0.05	0.79
ND1	30	50.24%	1.83	0.036	45.33%Potamalosa richmondia	50.62%	53.85%Escualosa thoracata	−0.29	0.12
ND2	30	50.75%	1.90	0.038	46.12%Dorosoma petenense	50.43%	54.45%Sardinella lemuru	−0.12	0.54
COX1	30	47.02%	1.21	0.026	44.87%Potamalosa richmondia	46.91%	49.52%Sardinella lemuru	−0.14	0.45
COX2	30	45.88%	1.20	0.026	43.70%Clupeonella abrau	45.88%	48.19%Harengula jaguana	−0.08	0.68
ATP8	30	43.65%	2.43	0.056	40.48%Alosa alosa	43.45%	48.81%Sardinella gibbosa	−0.17	0.38
ATP6	30	46.50%	1.62	0.035	43.78%Spratelloides gracilis	46.16%	50.58%Escualosa thoracata	0.08	0.66
COX3	30	49.67%	1.26	0.025	47.33%Tenualosa toli	49.43%	52.23%Sardina pilchardus	−0.01	0.95
ND3	30	47.56%	2.01	0.042	43.55%Dorosoma petenense	47.56%	51.00%Nematalosa erebi	−0.04	0.83
ND4L	30	50.75%	2.01	0.040	47.81%Alosa pseudoharengus	50.34%	55.22%Escualosa thoracata	−0.25	0.19
ND4	30	48.36%	1.93	0.040	43.95%Dorosoma petenense	48.66%	51.34%Escualosa thoracata	−0.09	0.64
ND5	30	47.10%	1.55	0.033	43.68%Potamalosa richmondia	46.98%	49.73%Escualosa thoracata	−0.15	0.44
ND6	30	48.55%	2.46	0.051	43.68%Dorosoma petenense	48.70%	52.87%Sardinella gibbosa	−0.10	0.61
CYTB	30	47.53%	1.61	0.034	44.26%Dorosoma petenense	47.60%	50.83%Sardina pilchardus	−0.18	0.34

Genera of Clupeidae

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

Region

Parameter

Chart

Genera of Clupeidae

Alosa	5	46.78%	0.29	0.006	46.47%Alosa pseudoharengus	46.75%	47.24%Alosa alosa	0.28	0.64
Sardinella	5	48.48%	0.92	0.019	47.60%Sardinella longiceps	48.04%	49.76%Sardinella lemuru	0.02	0.97
Clupea	2	47.38%	0.01	0.000	47.37%Clupea pallasii	47.38%	47.38%Clupea harengus	–	–
Clupeonella	2	47.11%	0.18	0.004	46.99%Clupeonella abrau	47.11%	47.24%Clupeonella cultriventris	–	–
Dorosoma	2	46.16%	1.21	0.026	45.30%Dorosoma petenense	46.16%	47.02%Dorosoma cepedianum	–	–
Tenualosa	2	48.17%	0.46	0.010	47.84%Tenualosa ilisha	48.17%	48.49%Tenualosa toli	–	–
Harengula	1	49.24%	–	–	49.24%Harengula jaguana	49.24%	49.24%Harengula jaguana	–	–
Potamalosa	1	45.29%	–	–	45.29%Potamalosa richmondia	45.29%	45.29%Potamalosa richmondia	–	–
Sardina	1	50.07%	–	–	50.07%Sardina pilchardus	50.07%	50.07%Sardina pilchardus	–	–
Sprattus	1	47.33%	–	–	47.33%Sprattus sprattus	47.33%	47.33%Sprattus sprattus	–	–
Sardinops	1	48.68%	–	–	48.68%Sardinops sagax	48.68%	48.68%Sardinops sagax	–	–
Opisthonema	1	47.77%	–	–	47.77%Opisthonema oglinum	47.77%	47.77%Opisthonema oglinum	–	–
Nematalosa	1	47.63%	–	–	47.63%Nematalosa erebi	47.63%	47.63%Nematalosa erebi	–	–
Spratelloides	1	48.12%	–	–	48.12%Spratelloides gracilis	48.12%	48.12%Spratelloides gracilis	–	–
Konosirus	1	48.80%	–	–	48.80%Konosirus punctatus	48.80%	48.80%Konosirus punctatus	–	–

Codon usage

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

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

Clupeidae 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.