order · mtDNA statistics

Decapoda

26 species in 13 families. Every region of their mitochondrial genomes, side by side.

Group

species

31.6%

mean GC, whole genome

SD 2.3, range 25.9–37.4%

15,997

median genome length, bp

Range 14,316–42,736 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	26	31.63%	2.34	0.074	25.92%Cancer pagurus	31.59%	37.37%Panulirus argus	−0.04	0.86
Protein-coding	26	33.61%	2.02	0.060	29.86%Chionoecetes bairdi	33.44%	39.29%Panulirus argus	0.03	0.89
All rRNA	26	28.17%	2.26	0.080	22.92%Eriocheir sinensis	28.69%	33.39%Panulirus argus	−0.21	0.31
All tRNA	26	30.63%	2.99	0.098	25.49%Cancer pagurus	29.87%	36.10%Aristaeomorpha foliacea	−0.21	0.31
12S rRNA	26	29.10%	2.61	0.090	23.43%Eriocheir sinensis	29.59%	34.72%Panulirus argus	−0.34	0.09
16S rRNA	26	27.59%	2.27	0.082	22.58%Eriocheir sinensis	27.35%	32.57%Panulirus argus	−0.10	0.64
D-loop	21	22.91%	4.35	0.190	16.52%Trachypenaeus curvirostris	21.74%	33.05%Trypaea australiensis	0.21	0.37
ND1	26	32.16%	1.82	0.056	29.36%Chionoecetes bairdi	31.97%	36.93%Panulirus argus	0.10	0.64
ND2	25	32.36%	2.53	0.078	26.74%Chionoecetes bairdi	32.44%	37.60%Panulirus argus	−0.00	1
COX1	26	37.41%	2.09	0.056	34.31%Charybdis hellerii	37.06%	43.94%Panulirus argus	0.09	0.65
COX2	26	35.68%	2.16	0.060	32.27%Cancer pagurus	35.76%	42.30%Panulirus argus	0.23	0.26
ATP8	26	26.21%	2.89	0.110	20.99%Eriocheir sinensis	26.54%	31.45%Cherax quadricarinatus	−0.16	0.43
ATP6	26	34.41%	2.21	0.064	29.33%Chionoecetes bairdi	34.07%	40.41%Panulirus argus	0.03	0.89
COX3	26	37.51%	2.13	0.057	33.71%Eriocheir sinensis	38.19%	41.97%Panulirus argus	−0.10	0.64
ND3	26	33.26%	2.86	0.086	27.12%Chionoecetes bairdi	33.43%	39.77%Panulirus argus	−0.16	0.43
ND4L	26	30.68%	2.52	0.082	25.74%Eriocheir sinensis	29.70%	35.97%Panulirus argus	0.13	0.54
ND4	26	31.03%	2.36	0.076	27.49%Portunus trituberculatus	30.79%	36.67%Panulirus argus	0.10	0.62
ND5	26	31.29%	2.14	0.068	26.39%Chionoecetes bairdi	31.25%	37.42%Panulirus argus	0.02	0.93
ND6	26	30.17%	3.01	0.100	23.81%Eriocheir sinensis	30.01%	36.05%Panulirus argus	0.01	0.97
CYTB	26	36.14%	2.47	0.068	32.42%Portunus trituberculatus	36.54%	41.23%Panulirus argus	−0.14	0.5

Families of Decapoda

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

Region

Parameter

Chart

Families of Decapoda

Portunidae	7	30.95%	1.63	0.053	29.78%Portunus trituberculatus	30.64%	34.40%Portunus sanguinolentus	0.15	0.75
Penaeidae	4	32.04%	0.59	0.018	31.33%Trachypenaeus curvirostris	32.02%	32.77%Penaeus duorarum	–	–
Solenoceridae	3	32.15%	0.32	0.010	31.78%Pleoticus muelleri	32.33%	32.33%Solenocera crassicornis	–	–
Nephropidae	2	30.94%	0.66	0.021	30.47%Homarus americanus	30.94%	31.41%Homarus gammarus	–	–
Cancridae	2	27.98%	2.92	0.104	25.92%Cancer pagurus	27.98%	30.05%Metacarcinus magister	–	–
Palinuridae	1	37.37%	–	–	37.37%Panulirus argus	37.37%	37.37%Panulirus argus	–	–
Parastacidae	1	34.58%	–	–	34.58%Cherax quadricarinatus	34.58%	34.58%Cherax quadricarinatus	–	–
Varunidae	1	28.37%	–	–	28.37%Eriocheir sinensis	28.37%	28.37%Eriocheir sinensis	–	–
Coenobitidae	1	34.36%	–	–	34.36%Birgus latro	34.36%	34.36%Birgus latro	–	–
Majidae	1	28.62%	–	–	28.62%Chionoecetes bairdi	28.62%	28.62%Chionoecetes bairdi	–	–
Palaemonidae	1	33.17%	–	–	33.17%Palaemon adspersus	33.17%	33.17%Palaemon adspersus	–	–
Callianassidae	1	32.78%	–	–	32.78%Trypaea australiensis	32.78%	32.78%Trypaea australiensis	–	–
Aristeidae	1	33.98%	–	–	33.98%Aristaeomorpha foliacea	33.98%	33.98%Aristaeomorpha foliacea	–	–

Codon usage

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

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

Decapoda 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.