class · mtDNA statistics

Reptilia

Reptiles: 136 species in 5 orders. Every region of their mitochondrial genomes, side by side.

Group

136

species

40.6%

mean GC, whole genome

SD 2.5, range 35.8–48.1%

16,859

median genome length, bp

Range 14,935–25,972 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	136	40.61%	2.50	0.062	35.81%Kinosternon leucostomum	40.18%	48.07%Gonatodes albogularis	0.05	0.55
Protein-coding	136	41.11%	2.65	0.064	35.18%Bungarus fasciatus	40.70%	48.11%Gonatodes albogularis	0.14	0.12
All rRNA	136	41.70%	2.57	0.062	36.57%Kinosternon leucostomum	40.92%	50.47%Gonatodes albogularis	−0.04	0.64
All tRNA	136	40.58%	2.33	0.057	34.42%Heloderma suspectum	40.58%	47.56%Gonatodes albogularis	−0.11	0.18
12S rRNA	135	43.46%	2.92	0.067	37.90%Heloderma suspectum	42.72%	51.32%Pogona vitticeps	0.04	0.66
16S rRNA	135	40.62%	2.62	0.065	35.32%Kinosternon leucostomum	40.09%	50.42%Gonatodes albogularis	−0.09	0.3
D-loop	116	34.44%	5.62	0.163	25.07%Gavialis gangeticus	33.13%	53.33%Gonatodes albogularis	−0.25	0.007
ND1	136	41.39%	2.98	0.072	35.50%Zootoca vivipara	40.93%	49.59%Paleosuchus palpebrosus	0.14	0.12
ND2	136	40.21%	3.12	0.078	33.78%Kinosternon leucostomum	39.65%	49.27%Lepidophyma flavimaculatum	0.13	0.12
COX1	136	42.60%	2.27	0.053	37.60%Chamaeleo dilepis	42.18%	49.61%Gonatodes albogularis	−0.02	0.84
COX2	136	41.12%	3.31	0.081	34.50%Chelydra serpentina	40.98%	50.29%Gonatodes albogularis	−0.09	0.31
ATP8	136	36.25%	4.61	0.127	26.71%Tropidophis haetianus	35.78%	48.52%Paleosuchus palpebrosus	0.11	0.22
ATP6	136	39.84%	3.26	0.082	32.45%Ptyas mucosa	39.53%	47.79%Hemitheconyx caudicinctus	0.14	0.12
COX3	136	43.54%	2.60	0.060	37.37%Chamaeleo chamaeleon	43.24%	50.38%Gonatodes albogularis	0.16	0.06
ND3	136	40.64%	3.55	0.087	32.36%Bungarus fasciatus	40.14%	49.42%Hoplodactylus duvaucelii	0.13	0.12
ND4L	136	40.34%	3.68	0.091	30.93%Coluber constrictor	40.03%	50.84%Gonatodes albogularis	0.28	0.001
ND4	136	40.49%	2.91	0.072	34.47%Heloderma suspectum	39.96%	48.80%Paleosuchus palpebrosus	0.04	0.63
ND5	135	40.08%	2.95	0.074	32.03%Bungarus fasciatus	39.52%	48.42%Gonatodes albogularis	0.21	0.01
ND6	136	40.10%	3.85	0.096	29.90%Kinosternon leucostomum	39.45%	50.19%Paleosuchus palpebrosus	0.19	0.02
CYTB	136	42.36%	2.61	0.062	35.46%Bungarus fasciatus	42.29%	50.48%Paleosuchus trigonatus	0.26	0.002

Orders of Reptilia

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

Region

Parameter

Chart

Orders of Reptilia

Squamata	65	41.17%	2.56	0.062	36.39%Bungarus fasciatus	41.27%	48.07%Gonatodes albogularis	0.19	0.14
Testudines	51	38.91%	1.09	0.028	35.81%Kinosternon leucostomum	38.79%	41.52%Trionyx triunguis	0.04	0.78
Crocodilia	18	43.27%	1.87	0.043	40.85%Osteolaemus tetraspis	42.93%	47.60%Paleosuchus palpebrosus	−0.28	0.25
Rhynchocephalia	1	39.86%	–	–	39.86%Sphenodon punctatus	39.86%	39.86%Sphenodon punctatus	–	–
Crocodylia	1	43.75%	–	–	43.75%Crocodylus johnstoni	43.75%	43.75%Crocodylus johnstoni	–	–

Codon usage

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

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

Reptilia 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.