family · mtDNA statistics

Sciaenidae

21 species in 16 genera. Every region of their mitochondrial genomes, side by side.

Group

species

47.0%

mean GC, whole genome

SD 1.0, range 44.2–48.6%

16,500

median genome length, bp

Range 16,466–16,589 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	21	47.05%	0.97	0.021	44.20%Pama pama	47.14%	48.64%Menticirrhus americanus	0.20	0.38
Protein-coding	21	47.99%	1.23	0.026	44.46%Pama pama	48.10%	50.11%Menticirrhus americanus	0.19	0.41
All rRNA	21	46.79%	0.54	0.012	45.52%Macrodon ancylodon	46.94%	47.51%Pseudotolithus typus	0.01	0.96
All tRNA	21	45.45%	0.45	0.010	44.19%Pama pama	45.47%	46.35%Umbrina canosai	0.43	0.05
12S rRNA	21	47.83%	0.74	0.015	46.26%Macrodon ancylodon	47.74%	49.26%Miichthys miiuy	−0.16	0.48
16S rRNA	20	46.20%	0.62	0.013	44.92%Pama pama	46.33%	47.17%Pseudotolithus elongatus	0.13	0.6
D-loop	19	35.91%	27.29	0.760	0.00%Micropogonias furnieri	36.92%	100.00%Macrodon ancylodon	−0.15	0.54
ND1	21	48.25%	1.52	0.031	44.82%Pama pama	48.41%	50.67%Menticirrhus americanus	0.17	0.45
ND2	21	48.55%	1.45	0.030	45.27%Otolithes ruber	48.76%	50.86%Miichthys miiuy	0.04	0.87
COX1	21	48.16%	1.37	0.028	44.38%Pama pama	48.06%	50.74%Menticirrhus americanus	0.02	0.92
COX2	21	45.48%	1.31	0.029	43.27%Pama pama	45.30%	48.77%Menticirrhus americanus	0.12	0.62
ATP8	21	42.64%	3.04	0.071	32.74%Pama pama	43.45%	47.62%Macrodon ancylodon	0.12	0.61
ATP6	21	47.95%	1.75	0.037	43.27%Pama pama	48.54%	51.32%Miichthys miiuy	0.29	0.2
COX3	21	48.86%	1.09	0.022	46.37%Pama pama	48.66%	50.57%Menticirrhus americanus	0.04	0.85
ND3	21	49.40%	2.27	0.046	43.84%Pama pama	49.86%	52.15%Argyrosomus japonicus	0.21	0.36
ND4L	21	51.37%	2.08	0.041	45.79%Otolithes ruber	51.85%	55.22%Larimichthys polyactis	0.27	0.24
ND4	21	48.91%	1.83	0.037	44.24%Pama pama	49.46%	51.70%Menticirrhus americanus	0.22	0.33
ND5	21	46.32%	1.46	0.032	42.90%Otolithes ruber	46.28%	48.67%Menticirrhus americanus	0.07	0.77
ND6	21	47.62%	1.43	0.030	45.40%Otolithes ruber	47.32%	50.96%Pennahia macrocephala	−0.17	0.46
CYTB	21	48.81%	1.31	0.027	45.22%Pama pama	48.90%	50.92%Totoaba macdonaldi	0.49	0.02

Genera of Sciaenidae

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

Region

Parameter

Chart

Genera of Sciaenidae

Micropogonias	2	46.90%	0.19	0.004	46.76%Micropogonias undulatus	46.90%	47.03%Micropogonias furnieri	–	–
Pennahia	2	46.71%	0.70	0.015	46.22%Pennahia argentata	46.71%	47.21%Pennahia macrocephala	–	–
Larimichthys	2	47.22%	0.33	0.007	46.99%Larimichthys crocea	47.22%	47.45%Larimichthys polyactis	–	–
Pseudotolithus	2	47.41%	0.71	0.015	46.91%Pseudotolithus elongatus	47.41%	47.91%Pseudotolithus typus	–	–
Cynoscion	2	47.36%	0.31	0.007	47.14%Cynoscion striatus	47.36%	47.58%Cynoscion jamaicensis	–	–
Argyrosomus	1	47.71%	–	–	47.71%Argyrosomus japonicus	47.71%	47.71%Argyrosomus japonicus	–	–
Sciaenops	1	47.07%	–	–	47.07%Sciaenops ocellatus	47.07%	47.07%Sciaenops ocellatus	–	–
Macrodon	1	46.36%	–	–	46.36%Macrodon ancylodon	46.36%	46.36%Macrodon ancylodon	–	–
Miichthys	1	48.08%	–	–	48.08%Miichthys miiuy	48.08%	48.08%Miichthys miiuy	–	–
Nibea	1	47.72%	–	–	47.72%Nibea albiflora	47.72%	47.72%Nibea albiflora	–	–
Totoaba	1	47.53%	–	–	47.53%Totoaba macdonaldi	47.53%	47.53%Totoaba macdonaldi	–	–
Menticirrhus	1	48.64%	–	–	48.64%Menticirrhus americanus	48.64%	48.64%Menticirrhus americanus	–	–
Otolithes	1	45.21%	–	–	45.21%Otolithes ruber	45.21%	45.21%Otolithes ruber	–	–
Protonibea	1	47.19%	–	–	47.19%Protonibea diacanthus	47.19%	47.19%Protonibea diacanthus	–	–
Umbrina	1	47.05%	–	–	47.05%Umbrina canosai	47.05%	47.05%Umbrina canosai	–	–

Codon usage

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

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

Sciaenidae 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.