family · mtDNA statistics

Portunidae

7 species in 4 genera. Every region of their mitochondrial genomes, side by side.

Group

species

30.9%

mean GC, whole genome

SD 1.6, range 29.8–34.4%

16,024

median genome length, bp

Range 15,660–16,263 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	7	30.95%	1.63	0.053	29.78%Portunus trituberculatus	30.64%	34.40%Portunus sanguinolentus	0.15	0.75
Protein-coding	7	32.68%	1.78	0.055	31.16%Charybdis hellerii	32.70%	36.22%Portunus sanguinolentus	0.07	0.88
All rRNA	7	28.02%	1.83	0.065	26.36%Scylla olivacea	27.62%	31.65%Portunus sanguinolentus	0.43	0.34
All tRNA	7	28.14%	0.38	0.014	27.53%Charybdis hellerii	28.28%	28.57%Portunus sanguinolentus	0.48	0.27
12S rRNA	7	29.56%	1.69	0.057	27.58%Scylla olivacea	29.68%	32.70%Portunus sanguinolentus	0.50	0.25
16S rRNA	7	27.04%	1.98	0.073	25.58%Scylla olivacea	26.20%	30.97%Portunus sanguinolentus	0.37	0.42
D-loop	7	23.69%	3.18	0.134	20.95%Scylla olivacea	23.64%	30.27%Portunus sanguinolentus	0.39	0.39
ND1	7	31.20%	1.11	0.036	29.99%Scylla olivacea	30.88%	32.92%Portunus sanguinolentus	0.56	0.19
ND2	7	31.93%	1.97	0.062	29.86%Charybdis hellerii	31.85%	35.91%Portunus sanguinolentus	0.04	0.93
COX1	7	36.60%	1.95	0.053	34.31%Charybdis hellerii	36.44%	40.16%Portunus sanguinolentus	0.02	0.96
COX2	7	35.41%	2.01	0.057	33.43%Charybdis feriata	35.47%	38.98%Portunus sanguinolentus	−0.02	0.96
ATP8	7	26.90%	3.47	0.129	22.22%Portunus trituberculatus	26.54%	30.86%Charybdis feriata	0.17	0.72
ATP6	7	33.50%	1.36	0.041	32.01%Charybdis feriata	33.78%	35.84%Portunus sanguinolentus	−0.13	0.79
COX3	7	36.00%	1.81	0.050	33.71%Portunus trituberculatus	35.86%	39.14%Portunus sanguinolentus	−0.02	0.97
ND3	7	32.81%	2.86	0.087	29.66%Charybdis feriata	32.49%	38.14%Portunus sanguinolentus	0.33	0.48
ND4L	7	30.88%	2.64	0.085	28.05%Scylla olivacea	30.36%	34.65%Portunus sanguinolentus	0.50	0.26
ND4	7	29.34%	2.20	0.075	27.49%Portunus trituberculatus	28.54%	33.71%Portunus sanguinolentus	−0.06	0.89
ND5	7	30.34%	1.73	0.057	28.88%Charybdis feriata	29.98%	33.64%Portunus sanguinolentus	0.17	0.71
ND6	7	29.36%	3.10	0.105	26.63%Portunus trituberculatus	27.42%	34.71%Portunus sanguinolentus	0.39	0.39
CYTB	7	34.80%	2.20	0.063	32.42%Portunus trituberculatus	34.01%	38.33%Portunus sanguinolentus	−0.35	0.44

Genera of Portunidae

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

Region

Parameter

Chart

Genera of Portunidae

Portunus	3	31.82%	2.36	0.074	29.78%Portunus trituberculatus	31.26%	34.40%Portunus sanguinolentus	–	–
Charybdis	2	29.83%	0.04	0.001	29.80%Charybdis hellerii	29.83%	29.85%Charybdis feriata	–	–
Callinectes	1	30.90%	–	–	30.90%Callinectes sapidus	30.90%	30.90%Callinectes sapidus	–	–
Scylla	1	30.64%	–	–	30.64%Scylla olivacea	30.64%	30.64%Scylla olivacea	–	–

Codon usage

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

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

Portunidae 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.