order · mtDNA statistics

Squamata

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

Group

species

41.2%

mean GC, whole genome

SD 2.6, range 36.4–48.1%

17,188

median genome length, bp

Range 16,129–25,972 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	65	41.17%	2.56	0.062	36.39%Bungarus fasciatus	41.27%	48.07%Gonatodes albogularis	0.19	0.14
Protein-coding	65	41.38%	2.91	0.070	35.18%Bungarus fasciatus	41.21%	48.11%Gonatodes albogularis	0.21	0.09
All rRNA	65	42.30%	2.51	0.059	37.31%Anolis carolinensis	42.03%	50.47%Gonatodes albogularis	−0.06	0.65
All tRNA	65	41.54%	1.95	0.047	34.42%Heloderma suspectum	41.24%	47.56%Gonatodes albogularis	−0.08	0.51
12S rRNA	64	43.96%	2.90	0.066	37.90%Heloderma suspectum	43.46%	51.32%Pogona vitticeps	−0.03	0.83
16S rRNA	64	41.28%	2.71	0.066	36.93%Anolis carolinensis	40.49%	50.42%Gonatodes albogularis	−0.07	0.58
D-loop	48	38.75%	4.69	0.121	27.26%Calotes versicolor	39.13%	53.33%Gonatodes albogularis	0.21	0.15
ND1	65	41.84%	2.96	0.071	35.50%Zootoca vivipara	41.81%	47.86%Gonatodes albogularis	0.27	0.03
ND2	65	40.56%	3.51	0.087	33.79%Bungarus fasciatus	40.64%	49.27%Lepidophyma flavimaculatum	0.28	0.02
COX1	65	43.36%	2.59	0.060	37.60%Chamaeleo dilepis	43.82%	49.61%Gonatodes albogularis	0.25	0.04
COX2	65	42.97%	3.02	0.070	35.33%Eublepharis macularius	43.38%	50.29%Gonatodes albogularis	0.33	0.007
ATP8	65	36.45%	5.25	0.144	26.71%Tropidophis haetianus	36.48%	46.67%Varanus salvator	0.10	0.42
ATP6	65	40.17%	3.73	0.093	32.45%Ptyas mucosa	40.09%	47.79%Hemitheconyx caudicinctus	0.17	0.17
COX3	65	43.87%	2.85	0.065	37.37%Chamaeleo chamaeleon	44.01%	50.38%Gonatodes albogularis	0.28	0.02
ND3	65	41.31%	3.77	0.091	32.36%Bungarus fasciatus	41.40%	49.42%Hoplodactylus duvaucelii	0.21	0.1
ND4L	65	39.28%	3.98	0.101	30.93%Coluber constrictor	38.83%	50.84%Gonatodes albogularis	0.14	0.27
ND4	65	40.98%	2.97	0.072	34.47%Heloderma suspectum	40.78%	47.51%Gonatodes albogularis	0.20	0.1
ND5	65	39.76%	3.24	0.081	32.03%Bungarus fasciatus	39.25%	48.42%Gonatodes albogularis	0.11	0.39
ND6	65	39.82%	4.06	0.102	30.74%Ptyas mucosa	39.53%	49.04%Heteronotia binoei	0.06	0.65
CYTB	65	41.69%	2.88	0.069	35.46%Bungarus fasciatus	41.76%	47.93%Gonatodes albogularis	0.14	0.26

Families of Squamata

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

Region

Parameter

Chart

Families of Squamata

Viperidae	13	41.33%	1.20	0.029	39.21%Daboia russelii	41.72%	42.93%Crotalus adamanteus	0.60	0.03
Colubridae	8	39.62%	1.55	0.039	37.15%Ptyas mucosa	39.33%	41.84%Nerodia sipedon	−0.28	0.5
Elapidae	6	40.15%	2.24	0.056	36.39%Bungarus fasciatus	41.42%	41.70%Naja naja	0.53	0.28
Agamidae	4	41.64%	1.15	0.028	40.26%Calotes versicolor	41.63%	43.04%Pogona vitticeps	–	–
Eublepharidae	3	42.14%	4.70	0.111	36.84%Eublepharis macularius	43.77%	45.80%Hemitheconyx caudicinctus	–	–
Gekkonidae	3	41.53%	2.12	0.051	39.55%Phelsuma guimbeaui	41.27%	43.77%Heteronotia binoei	–	–
Lacertidae	3	38.51%	1.73	0.045	36.76%Zootoca vivipara	38.55%	40.23%Lacerta viridis	–	–
Pythonidae	3	41.46%	1.06	0.025	40.25%Malayopython reticulatus	41.94%	42.19%Python molurus	–	–
Anguidae	2	44.85%	0.00	0.000	44.85%Pseudopus apodus	44.85%	44.85%Anguis fragilis	–	–
Chamaeleonidae	2	37.77%	0.88	0.023	37.15%Chamaeleo dilepis	37.77%	38.39%Chamaeleo chamaeleon	–	–
Iguanidae	2	44.99%	0.26	0.006	44.81%Amblyrhynchus cristatus	44.99%	45.18%Iguana iguana	–	–
Varanidae	2	42.63%	2.11	0.050	41.14%Varanus niloticus	42.63%	44.12%Varanus salvator	–	–
Blanidae	1	44.32%	–	–	44.32%Blanus cinereus	44.32%	44.32%Blanus cinereus	–	–
Boidae	1	38.49%	–	–	38.49%Boa constrictor	38.49%	38.49%Boa constrictor	–	–
Corytophanidae	1	40.73%	–	–	40.73%Basiliscus vittatus	40.73%	40.73%Basiliscus vittatus	–	–

Codon usage

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

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

Squamata 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.