class · mtDNA statistics

Bivalvia

Bivalves: 35 species in 11 orders. Every region of their mitochondrial genomes, side by side.

Group

species

36.4%

mean GC, whole genome

SD 4.3, range 28.3–44.9%

17,492

median genome length, bp

Range 14,622–48,161 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	35	36.41%	4.32	0.119	28.27%Geukensia demissa	36.25%	44.92%Cryolaternula elliptica	−0.29	0.09
Protein-coding	35	37.04%	3.97	0.107	29.40%Geukensia demissa	36.84%	44.96%Cryolaternula elliptica	−0.27	0.11
All rRNA	35	36.25%	4.73	0.131	27.82%Geukensia demissa	35.09%	44.97%Mimachlamys varia	−0.43	0.01
All tRNA	35	37.61%	6.09	0.162	28.93%Mercenaria mercenaria	35.83%	51.01%Ylistrum balloti	−0.38	0.03
12S rRNA	35	38.28%	5.35	0.140	28.25%Geukensia demissa	36.84%	47.94%Tegillarca granosa	−0.38	0.02
16S rRNA	35	34.66%	4.86	0.140	26.54%Corbicula japonica	34.25%	44.06%Cryolaternula elliptica	−0.43	0.01
D-loop	7	32.37%	10.63	0.328	10.06%Amusium pleuronectes	36.31%	40.19%Ylistrum balloti	0.23	0.62
ND1	35	37.19%	3.50	0.094	28.62%Geukensia demissa	36.90%	43.94%Mimachlamys varia	−0.18	0.3
ND2	35	36.00%	4.99	0.139	26.90%Geukensia demissa	35.53%	46.33%Cryolaternula elliptica	−0.31	0.07
COX1	35	38.16%	2.88	0.075	33.33%Geukensia demissa	38.01%	45.01%Mimachlamys varia	−0.18	0.29
COX2	35	38.11%	4.20	0.110	31.09%Arctica islandica	38.10%	46.75%Cerastoderma edule	−0.30	0.08
ATP8	17	33.57%	5.50	0.164	25.52%Anodonta anatina	32.89%	44.65%Mimachlamys varia	−0.00	1
ATP6	35	35.71%	4.53	0.127	27.53%Corbicula fluminea	35.05%	45.11%Cryolaternula elliptica	−0.23	0.19
COX3	35	38.96%	3.75	0.096	32.43%Ruditapes philippinarum	39.16%	45.82%Cryolaternula elliptica	−0.25	0.14
ND3	35	37.58%	5.49	0.146	27.41%Ruditapes philippinarum	36.97%	49.12%Pinna rudis	−0.16	0.35
ND4L	35	36.02%	6.66	0.185	23.53%Ruditapes philippinarum	36.10%	50.17%Placopecten magellanicus	−0.28	0.11
ND4	35	36.88%	4.01	0.109	27.20%Geukensia demissa	36.58%	45.17%Mimachlamys varia	−0.28	0.11
ND5	35	36.29%	4.86	0.134	27.18%Geukensia demissa	35.71%	46.08%Placopecten magellanicus	−0.28	0.1
ND6	35	36.28%	5.57	0.154	26.28%Geukensia demissa	35.27%	48.43%Cryolaternula elliptica	−0.36	0.03
CYTB	35	36.88%	3.76	0.102	29.81%Corbicula fluminea	36.94%	44.00%Mimachlamys varia	−0.21	0.24

Orders of Bivalvia

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

Region

Parameter

Chart

Orders of Bivalvia

Mytilida	7	35.58%	3.43	0.096	28.27%Geukensia demissa	36.19%	38.46%Mytilus trossulus	−0.21	0.66
Venerida	6	31.27%	2.52	0.081	29.52%Corbicula fluminea	30.55%	36.27%Mactra chinensis	−0.02	0.97
Pectinida	5	42.41%	1.99	0.047	39.18%Amusium pleuronectes	42.72%	44.33%Placopecten magellanicus	0.75	0.14
Ostreida	4	36.10%	0.94	0.026	35.14%Ostrea edulis	36.07%	37.13%Magallana ariakensis	–	–
Cardiida	3	38.64%	2.75	0.071	36.43%Macoma balthica	37.78%	41.73%Cerastoderma edule	–	–
Unionida	3	34.05%	0.06	0.002	33.99%Anodonta anatina	34.09%	34.09%Prolasmidonta heterodon	–	–
Adapedonta	2	35.93%	0.45	0.013	35.61%Panopea abrupta	35.93%	36.25%Panopea generosa	–	–
Arcoida	2	35.93%	5.50	0.153	32.04%Anadara kagoshimensis	35.93%	39.82%Tegillarca granosa	–	–
Myida	1	34.30%	–	–	34.30%Mya arenaria	34.30%	34.30%Mya arenaria	–	–
Pterioida	1	40.37%	–	–	40.37%Pinna rudis	40.37%	40.37%Pinna rudis	–	–

Codon usage

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

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

Bivalvia taxon page Plot GC content against GC skew 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.