family · mtDNA statistics

Viperidae

13 species in 10 genera. Every region of their mitochondrial genomes, side by side.

Group

species

41.3%

mean GC, whole genome

SD 1.2, range 39.2–42.9%

17,220

median genome length, bp

Range 16,269–17,388 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	13	41.33%	1.20	0.029	39.21%Daboia russelii	41.72%	42.93%Crotalus adamanteus	0.60	0.03
Protein-coding	13	41.80%	1.45	0.035	39.12%Daboia russelii	41.83%	43.65%Crotalus adamanteus	0.61	0.03
All rRNA	13	40.97%	1.05	0.026	39.69%Daboia russelii	40.69%	42.68%Crotalus adamanteus	0.44	0.13
All tRNA	13	40.99%	0.56	0.014	39.47%Daboia russelii	41.09%	41.87%Ovophis okinavensis	0.26	0.39
12S rRNA	12	42.25%	1.87	0.044	40.35%Echis carinatus	41.73%	46.05%Crotalus adamanteus	0.07	0.83
16S rRNA	12	40.01%	0.81	0.020	38.63%Trimeresurus albolabris	40.09%	41.45%Agkistrodon contortrix	0.59	0.04
D-loop	9	39.20%	1.46	0.037	36.98%Trimeresurus albolabris	38.90%	41.58%Sistrurus catenatus	0.23	0.54
ND1	13	42.32%	1.46	0.035	40.89%Daboia russelii	41.94%	45.06%Agkistrodon contortrix	0.52	0.07
ND2	13	41.28%	1.95	0.047	38.74%Trimeresurus albolabris	41.65%	43.98%Crotalus adamanteus	0.46	0.11
COX1	13	43.92%	1.16	0.026	41.32%Daboia russelii	43.92%	45.57%Crotalus adamanteus	0.50	0.08
COX2	13	44.88%	2.00	0.045	41.02%Daboia russelii	45.55%	47.59%Agkistrodon piscivorus	0.28	0.36
ATP8	13	35.99%	2.55	0.071	30.91%Daboia russelii	36.97%	40.61%Agkistrodon piscivorus	0.60	0.03
ATP6	13	40.84%	2.14	0.052	37.30%Daboia russelii	40.53%	44.35%Agkistrodon piscivorus	0.49	0.09
COX3	13	43.70%	1.47	0.034	40.05%Daboia russelii	43.73%	45.66%Protobothrops flavoviridis	0.54	0.05
ND3	13	41.44%	1.60	0.039	38.78%Daboia russelii	41.40%	44.01%Crotalus adamanteus	0.53	0.06
ND4L	13	39.11%	1.97	0.050	35.05%Daboia russelii	39.86%	41.58%Crotalus horridus	0.62	0.02
ND4	13	41.47%	1.95	0.047	39.01%Daboia russelii	41.78%	45.05%Crotalus horridus	0.58	0.04
ND5	13	39.68%	1.83	0.046	36.07%Trimeresurus albolabris	39.10%	41.94%Crotalus horridus	0.63	0.02
ND6	13	40.34%	2.65	0.066	37.57%Trimeresurus albolabris	40.80%	44.06%Crotalus horridus	0.34	0.26
CYTB	13	41.99%	1.37	0.033	39.59%Daboia russelii	42.28%	44.40%Crotalus adamanteus	0.43	0.14

Genera of Viperidae

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

Region

Parameter

Chart

Genera of Viperidae

Agkistrodon	2	42.36%	0.11	0.002	42.28%Agkistrodon piscivorus	42.36%	42.43%Agkistrodon contortrix	–	–
Crotalus	2	42.92%	0.02	0.000	42.90%Crotalus horridus	42.92%	42.93%Crotalus adamanteus	–	–
Echis	2	40.64%	0.01	0.000	40.64%Echis carinatus	40.64%	40.65%Echis coloratus	–	–
Daboia	1	39.21%	–	–	39.21%Daboia russelii	39.21%	39.21%Daboia russelii	–	–
Ovophis	1	41.82%	–	–	41.82%Ovophis okinavensis	41.82%	41.82%Ovophis okinavensis	–	–
Trimeresurus	1	39.56%	–	–	39.56%Trimeresurus albolabris	39.56%	39.56%Trimeresurus albolabris	–	–
Lachesis	1	40.69%	–	–	40.69%Lachesis muta	40.69%	40.69%Lachesis muta	–	–
Sistrurus	1	41.72%	–	–	41.72%Sistrurus catenatus	41.72%	41.72%Sistrurus catenatus	–	–
Vipera	1	40.65%	–	–	40.65%Vipera berus	40.65%	40.65%Vipera berus	–	–
Protobothrops	1	41.86%	–	–	41.86%Protobothrops flavoviridis	41.86%	41.86%Protobothrops flavoviridis	–	–

Codon usage

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

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

Viperidae 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.