family · mtDNA statistics

Trionychidae

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

Group

species

39.4%

mean GC, whole genome

SD 1.2, range 38.6–41.5%

16,749

median genome length, bp

Range 16,490–17,243 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	5	39.35%	1.24	0.031	38.58%Lissemys punctata	38.81%	41.52%Trionyx triunguis	0.68	0.2
Protein-coding	5	40.21%	1.56	0.039	38.85%Lissemys punctata	39.80%	42.77%Trionyx triunguis	0.67	0.21
All rRNA	5	39.54%	0.90	0.023	38.75%Apalone ferox	39.45%	41.01%Trionyx triunguis	0.61	0.27
All tRNA	5	38.40%	0.84	0.022	37.41%Apalone ferox	38.06%	39.53%Trionyx triunguis	0.27	0.67
12S rRNA	5	41.31%	0.77	0.019	40.31%Apalone spinifera	41.23%	42.48%Trionyx triunguis	0.67	0.21
16S rRNA	5	38.46%	1.04	0.027	37.31%Apalone ferox	38.28%	40.11%Trionyx triunguis	0.55	0.34
D-loop	5	32.76%	1.34	0.041	30.63%Apalone spinifera	32.93%	34.27%Palea steindachneri	0.29	0.63
ND1	5	40.28%	2.11	0.052	38.08%Lissemys punctata	40.08%	43.52%Trionyx triunguis	0.82	0.09
ND2	5	37.58%	1.41	0.038	35.42%Lissemys punctata	37.73%	39.36%Trionyx triunguis	0.82	0.09
COX1	5	42.18%	0.97	0.023	41.28%Lissemys punctata	42.02%	43.47%Trionyx triunguis	0.48	0.41
COX2	5	38.75%	1.73	0.045	36.97%Palea steindachneri	38.43%	41.63%Trionyx triunguis	0.47	0.43
ATP8	5	34.67%	1.24	0.036	33.33%Apalone ferox	35.15%	35.76%Palea steindachneri	0.52	0.37
ATP6	5	39.82%	2.66	0.067	36.11%Lissemys punctata	40.20%	42.98%Trionyx triunguis	0.64	0.24
COX3	5	43.68%	1.73	0.040	42.35%Lissemys punctata	43.28%	46.68%Trionyx triunguis	0.81	0.1
ND3	5	39.71%	1.38	0.035	38.11%Apalone spinifera	39.26%	41.83%Trionyx triunguis	0.48	0.42
ND4L	5	39.66%	3.28	0.083	35.02%Palea steindachneri	39.39%	44.11%Trionyx triunguis	0.17	0.79
ND4	5	39.35%	2.35	0.060	37.15%Palea steindachneri	38.96%	43.30%Trionyx triunguis	0.53	0.36
ND5	5	40.08%	1.19	0.030	39.01%Apalone ferox	39.52%	41.88%Trionyx triunguis	0.52	0.37
ND6	5	38.35%	1.72	0.045	36.57%Lissemys punctata	38.07%	41.14%Trionyx triunguis	0.84	0.07
CYTB	5	41.46%	1.86	0.045	39.65%Lissemys punctata	41.11%	44.21%Trionyx triunguis	0.61	0.28

Genera of Trionychidae

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

Region

Parameter

Chart

Genera of Trionychidae

Apalone	2	39.01%	0.28	0.007	38.81%Apalone ferox	39.01%	39.21%Apalone spinifera	–	–
Lissemys	1	38.58%	–	–	38.58%Lissemys punctata	38.58%	38.58%Lissemys punctata	–	–
Palea	1	38.63%	–	–	38.63%Palea steindachneri	38.63%	38.63%Palea steindachneri	–	–
Trionyx	1	41.52%	–	–	41.52%Trionyx triunguis	41.52%	41.52%Trionyx triunguis	–	–

Codon usage

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

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

Trionychidae 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.