family · mtDNA statistics

Geoemydidae

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

Group

species

38.9%

mean GC, whole genome

SD 0.9, range 37.5–40.6%

16,642

median genome length, bp

Range 16,443–17,067 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	16	38.93%	0.86	0.022	37.50%Notochelys platynota	39.01%	40.56%Geoclemys hamiltonii	0.18	0.5
Protein-coding	16	39.83%	0.87	0.022	38.06%Heosemys grandis	39.95%	41.12%Geoclemys hamiltonii	0.22	0.41
All rRNA	16	40.08%	0.80	0.020	38.39%Heosemys annandalii	40.23%	41.05%Mauremys sinensis	0.50	0.05
All tRNA	16	38.08%	0.61	0.016	37.33%Mauremys mutica	37.96%	39.94%Geoclemys hamiltonii	0.18	0.5
12S rRNA	16	41.16%	0.87	0.021	39.71%Heosemys annandalii	41.02%	42.96%Geoclemys hamiltonii	0.48	0.06
16S rRNA	16	39.42%	0.91	0.023	37.60%Heosemys annandalii	39.69%	40.74%Mauremys sinensis	0.42	0.11
D-loop	16	28.93%	3.06	0.106	25.27%Mauremys caspica	28.14%	33.91%Geoclemys hamiltonii	−0.19	0.48
ND1	16	39.24%	1.29	0.033	36.66%Heosemys grandis	39.06%	41.01%Geoclemys hamiltonii	0.30	0.26
ND2	16	39.17%	1.07	0.027	37.05%Notochelys platynota	39.28%	41.10%Geoclemys hamiltonii	0.16	0.56
COX1	16	41.57%	0.77	0.018	39.99%Heosemys grandis	41.51%	43.33%Geoclemys hamiltonii	0.15	0.58
COX2	16	37.90%	1.37	0.036	35.23%Notochelys platynota	37.98%	40.17%Cuora trifasciata	0.15	0.58
ATP8	16	35.15%	2.77	0.079	29.10%Notochelys platynota	35.12%	41.07%Mauremys annamensis	0.25	0.34
ATP6	16	37.88%	1.11	0.029	36.11%Mauremys leprosa	37.79%	40.35%Geoclemys hamiltonii	0.02	0.94
COX3	16	41.70%	0.78	0.019	40.43%Cuora flavomarginata	41.71%	43.11%Mauremys annamensis	0.18	0.5
ND3	16	37.38%	1.54	0.041	33.81%Cyclemys dentata	37.39%	39.94%Geoclemys hamiltonii	0.10	0.7
ND4L	16	40.63%	1.78	0.044	36.67%Heosemys grandis	40.67%	43.67%Mauremys annamensis	0.14	0.6
ND4	16	39.28%	1.12	0.029	37.18%Notochelys platynota	39.51%	41.10%Mauremys annamensis	0.30	0.27
ND5	16	39.17%	0.91	0.023	37.16%Heosemys grandis	39.34%	40.25%Cuora amboinensis	0.12	0.65
ND6	16	38.37%	1.59	0.042	34.67%Heosemys grandis	38.56%	40.76%Mauremys sinensis	0.03	0.92
CYTB	16	42.87%	1.01	0.023	40.82%Heosemys grandis	43.14%	44.14%Mauremys annamensis	0.24	0.37

Genera of Geoemydidae

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

Region

Parameter

Chart

Genera of Geoemydidae

Mauremys	7	39.22%	0.63	0.016	38.10%Mauremys leprosa	39.43%	39.97%Mauremys sinensis	−0.06	0.9
Cuora	3	39.02%	0.60	0.015	38.33%Cuora flavomarginata	39.32%	39.42%Cuora amboinensis	–	–
Heosemys	2	37.88%	0.38	0.010	37.62%Heosemys grandis	37.88%	38.15%Heosemys annandalii	–	–
Cyclemys	1	38.50%	–	–	38.50%Cyclemys dentata	38.50%	38.50%Cyclemys dentata	–	–
Notochelys	1	37.50%	–	–	37.50%Notochelys platynota	37.50%	37.50%Notochelys platynota	–	–
Sacalia	1	38.95%	–	–	38.95%Sacalia bealei	38.95%	38.95%Sacalia bealei	–	–
Geoclemys	1	40.56%	–	–	40.56%Geoclemys hamiltonii	40.56%	40.56%Geoclemys hamiltonii	–	–

Codon usage

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

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

Geoemydidae 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.