family · mtDNA statistics

Sciuridae

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

Group

species

37.5%

mean GC, whole genome

SD 1.5, range 35.1–39.9%

16,510

median genome length, bp

Range 16,299–16,674 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	24	37.50%	1.46	0.039	35.08%Tamias sibiricus	37.49%	39.92%Sundasciurus hippurus	0.56	0.004
Protein-coding	24	37.71%	1.68	0.045	34.78%Tamias sibiricus	37.61%	40.69%Sundasciurus hippurus	0.52	0.009
All rRNA	24	37.71%	1.27	0.034	35.92%Tamias striatus	37.34%	39.88%Ratufa bicolor	0.58	0.003
All tRNA	24	35.22%	0.92	0.026	33.60%Tamias striatus	35.12%	36.78%Callosciurus finlaysonii	0.65	6.3 × 10⁻⁴
12S rRNA	24	40.20%	1.71	0.043	37.97%Ictidomys tridecemlineatus	39.44%	43.70%Ratufa bicolor	0.49	0.02
16S rRNA	24	36.19%	1.15	0.032	34.37%Tamias striatus	36.09%	38.25%Petaurista alborufus	0.59	0.003
D-loop	23	37.45%	5.33	0.142	24.29%Callosciurus prevostii	37.62%	49.37%Marmota flaviventris	0.05	0.81
ND1	24	39.22%	1.96	0.050	35.98%Ictidomys tridecemlineatus	39.28%	42.53%Sundasciurus hippurus	0.30	0.16
ND2	24	35.32%	1.92	0.054	32.05%Spermophilus citellus	35.51%	39.54%Sundasciurus hippurus	0.45	0.03
COX1	24	39.09%	1.54	0.039	36.58%Tamias striatus	38.65%	41.76%Callosciurus finlaysonii	0.53	0.008
COX2	24	37.58%	1.78	0.047	35.23%Tamias sibiricus	37.21%	40.79%Petaurista alborufus	0.54	0.007
ATP8	24	33.76%	2.98	0.088	28.43%Tamias striatus	33.33%	38.24%Sundasciurus hippurus	0.33	0.12
ATP6	24	37.35%	2.05	0.055	34.07%Tamias striatus	37.40%	40.38%Callosciurus erythraeus	0.52	0.01
COX3	24	40.79%	1.60	0.039	37.37%Tamias sibiricus	40.93%	43.37%Petaurista alborufus	0.49	0.02
ND3	24	37.18%	2.54	0.068	32.66%Tamias sibiricus	36.83%	43.80%Petaurista alborufus	0.47	0.02
ND4L	24	34.33%	2.39	0.070	29.97%Tamias sibiricus	34.01%	40.40%Petaurista alborufus	0.48	0.02
ND4	24	35.94%	1.73	0.048	33.38%Spermophilus citellus	35.56%	38.97%Callosciurus finlaysonii	0.51	0.01
ND5	24	36.91%	1.88	0.051	32.62%Tamias sibiricus	37.13%	40.15%Sundasciurus hippurus	0.49	0.02
ND6	24	36.03%	1.58	0.044	32.38%Spermophilus citellus	36.29%	39.81%Sundasciurus hippurus	0.47	0.02
CYTB	24	40.63%	2.01	0.050	37.54%Spermophilus citellus	40.39%	44.30%Callosciurus erythraeus	0.46	0.02

Genera of Sciuridae

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

Region

Parameter

Chart

Genera of Sciuridae

Callosciurus	4	39.00%	0.40	0.010	38.61%Callosciurus notatus	39.00%	39.41%Callosciurus finlaysonii	–	–
Sciurus	4	37.53%	0.36	0.010	37.03%Sciurus vulgaris	37.61%	37.87%Sciurus variegatoides	–	–
Tamias	3	35.60%	0.74	0.021	35.08%Tamias sibiricus	35.29%	36.44%Tamias dorsalis	–	–
Marmota	3	36.20%	0.16	0.005	36.01%Marmota vancouverensis	36.28%	36.30%Marmota monax	–	–
Sundasciurus	2	39.11%	1.14	0.029	38.30%Sundasciurus lowii	39.11%	39.92%Sundasciurus hippurus	–	–
Cynomys	1	37.37%	–	–	37.37%Cynomys ludovicianus	37.37%	37.37%Cynomys ludovicianus	–	–
Ictidomys	1	36.32%	–	–	36.32%Ictidomys tridecemlineatus	36.32%	36.32%Ictidomys tridecemlineatus	–	–
Petaurista	1	39.61%	–	–	39.61%Petaurista alborufus	39.61%	39.61%Petaurista alborufus	–	–
Pteromys	1	37.43%	–	–	37.43%Pteromys volans	37.43%	37.43%Pteromys volans	–	–
Ratufa	1	39.68%	–	–	39.68%Ratufa bicolor	39.68%	39.68%Ratufa bicolor	–	–
Spermophilus	1	35.41%	–	–	35.41%Spermophilus citellus	35.41%	35.41%Spermophilus citellus	–	–
Glaucomys	1	37.61%	–	–	37.61%Glaucomys volans	37.61%	37.61%Glaucomys volans	–	–
Callospermophilus	1	36.81%	–	–	36.81%Callospermophilus lateralis	36.81%	36.81%Callospermophilus lateralis	–	–

Codon usage

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

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

Sciuridae 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.