class · mtDNA statistics

Malacostraca

Crustaceans: 30 species in 3 orders. Every region of their mitochondrial genomes, side by side.

Group

species

31.3%

mean GC, whole genome

SD 2.3, range 25.9–37.4%

15,983

median genome length, bp

Range 14,316–42,736 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	30	31.32%	2.33	0.074	25.92%Cancer pagurus	31.30%	37.37%Panulirus argus	0.08	0.68
Protein-coding	30	33.29%	2.07	0.062	29.86%Chionoecetes bairdi	33.30%	39.29%Panulirus argus	0.16	0.4
All rRNA	30	27.81%	2.38	0.085	22.76%Euphausia pacifica	27.95%	33.39%Panulirus argus	−0.05	0.78
All tRNA	30	30.50%	2.84	0.093	25.49%Cancer pagurus	29.87%	36.10%Aristaeomorpha foliacea	−0.15	0.42
12S rRNA	30	28.94%	2.57	0.089	23.43%Eriocheir sinensis	29.46%	34.72%Panulirus argus	−0.24	0.2
16S rRNA	30	27.11%	2.48	0.092	22.02%Euphausia pacifica	26.74%	32.57%Panulirus argus	0.07	0.71
D-loop	24	22.51%	4.29	0.191	16.52%Trachypenaeus curvirostris	21.65%	33.05%Trypaea australiensis	0.30	0.16
ND1	30	31.96%	1.92	0.060	28.33%Euphausia pacifica	31.84%	36.93%Panulirus argus	0.14	0.45
ND2	29	32.05%	2.48	0.077	26.74%Chionoecetes bairdi	31.93%	37.60%Panulirus argus	0.10	0.59
COX1	30	37.18%	2.05	0.055	34.31%Charybdis hellerii	36.64%	43.94%Panulirus argus	0.20	0.3
COX2	30	35.30%	2.26	0.064	31.69%Euphausia pacifica	35.40%	42.30%Panulirus argus	0.31	0.1
ATP8	30	25.85%	2.89	0.112	20.99%Eriocheir sinensis	25.79%	31.45%Cherax quadricarinatus	−0.04	0.82
ATP6	30	33.93%	2.40	0.071	29.33%Chionoecetes bairdi	34.07%	40.41%Panulirus argus	0.19	0.31
COX3	30	37.15%	2.19	0.059	33.71%Eriocheir sinensis	37.18%	41.97%Panulirus argus	0.05	0.8
ND3	30	32.86%	2.86	0.087	27.12%Chionoecetes bairdi	32.34%	39.77%Panulirus argus	−0.03	0.87
ND4L	30	30.47%	2.56	0.084	25.67%Euphausia pacifica	29.70%	35.97%Panulirus argus	0.19	0.31
ND4	30	30.83%	2.30	0.074	27.49%Portunus trituberculatus	30.57%	36.67%Panulirus argus	0.17	0.38
ND5	30	30.98%	2.17	0.070	26.39%Chionoecetes bairdi	30.83%	37.42%Panulirus argus	0.14	0.45
ND6	30	29.31%	3.68	0.125	20.96%Oratosquilla oratoria	29.54%	36.05%Panulirus argus	0.23	0.22
CYTB	30	35.81%	2.55	0.071	30.69%Euphausia pacifica	35.82%	41.23%Panulirus argus	0.00	1

Orders of Malacostraca

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

Region

Parameter

Chart

Orders of Malacostraca

Decapoda	26	31.63%	2.34	0.074	25.92%Cancer pagurus	31.59%	37.37%Panulirus argus	−0.04	0.86
Stomatopoda	3	29.76%	0.53	0.018	29.21%Oratosquilla oratoria	29.81%	30.26%Harpiosquilla harpax	–	–
Euphausiacea	1	28.03%	–	–	28.03%Euphausia pacifica	28.03%	28.03%Euphausia pacifica	–	–

Codon usage

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

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

Malacostraca 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.