order · mtDNA statistics

Rodentia

87 species in 17 families. Every region of their mitochondrial genomes, side by side.

Group

species

37.9%

mean GC, whole genome

SD 1.9, range 34.6–41.7%

16,413

median genome length, bp

Range 15,988–16,874 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	87	37.89%	1.87	0.049	34.56%Muscardinus avellanarius	37.54%	41.68%Castor canadensis	0.18	0.09
Protein-coding	87	38.27%	2.16	0.056	34.33%Proechimys brevicauda	37.90%	42.75%Castor canadensis	0.11	0.31
All rRNA	87	37.60%	1.52	0.040	34.18%Mus minutoides	37.47%	40.85%Ellobius talpinus	0.30	0.005
All tRNA	87	35.33%	1.29	0.036	32.74%Muscardinus avellanarius	35.08%	38.27%Castor canadensis	0.36	6.4 × 10⁻⁴
12S rRNA	87	39.12%	1.75	0.045	35.22%Apodemus peninsulae	39.08%	43.70%Ratufa bicolor	0.50	8.4 × 10⁻⁷
16S rRNA	87	36.66%	1.70	0.046	32.87%Mus minutoides	36.44%	40.33%Ellobius talpinus	0.12	0.29
D-loop	73	37.61%	3.64	0.097	24.29%Callosciurus prevostii	37.35%	49.37%Marmota flaviventris	0.22	0.06
ND1	87	39.38%	2.28	0.058	35.18%Cricetulus barabensis	39.37%	43.46%Castor canadensis	0.11	0.29
ND2	87	35.97%	2.63	0.073	30.70%Apodemus peninsulae	35.74%	41.18%Sigmodon hispidus	0.11	0.31
COX1	87	40.20%	2.15	0.053	36.32%Proechimys brevicauda	39.82%	45.18%Castor canadensis	−0.01	0.93
COX2	87	38.18%	2.38	0.062	31.58%Proechimys brevicauda	38.16%	42.69%Ellobius talpinus	0.04	0.72
ATP8	87	33.29%	2.65	0.079	27.94%Micaelamys namaquensis	33.33%	40.20%Cricetus cricetus	0.15	0.17
ATP6	87	37.97%	2.61	0.069	32.60%Proechimys brevicauda	37.89%	43.61%Chinchilla lanigera	0.15	0.18
COX3	87	41.13%	2.05	0.050	37.24%Glis glis	40.94%	46.17%Heterocephalus glaber	0.16	0.13
ND3	87	37.00%	2.94	0.080	30.92%Proechimys brevicauda	36.31%	44.51%Fukomys damarensis	0.32	0.003
ND4L	87	36.74%	3.49	0.095	27.61%Muscardinus avellanarius	36.36%	45.12%Lasiopodomys brandtii	−0.16	0.15
ND4	87	36.79%	2.48	0.067	30.84%Muscardinus avellanarius	36.43%	43.47%Heterocephalus glaber	0.11	0.32
ND5	87	37.26%	2.31	0.062	32.62%Tamias sibiricus	37.13%	42.00%Microtus ochrogaster	0.11	0.31
ND6	87	36.66%	2.30	0.063	31.79%Mus minutoides	36.72%	41.95%Lasiopodomys brandtii	−0.03	0.78
CYTB	87	40.60%	2.23	0.055	35.70%Proechimys brevicauda	40.38%	45.44%Castor canadensis	0.26	0.02

Families of Rodentia

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

Region

Parameter

Chart

Families of Rodentia

Sciuridae	24	37.50%	1.46	0.039	35.08%Tamias sibiricus	37.49%	39.92%Sundasciurus hippurus	0.56	0.004
Cricetidae	21	38.59%	1.91	0.049	35.30%Podomys floridanus	38.63%	41.33%Ellobius talpinus	−0.35	0.12
Muridae	20	37.12%	1.51	0.041	34.80%Apodemus peninsulae	36.93%	40.61%Acomys cahirinus	0.11	0.66
Gliridae	3	36.07%	1.45	0.040	34.56%Muscardinus avellanarius	36.19%	37.45%Eliomys quercinus	–	–
Bathyergidae	2	41.24%	0.01	0.000	41.23%Fukomys damarensis	41.24%	41.24%Heterocephalus glaber	–	–
Caviidae	2	39.17%	0.20	0.005	39.03%Cavia aperea	39.17%	39.31%Cavia porcellus	–	–
Octodontidae	2	37.19%	0.33	0.009	36.95%Spalacopus cyanus	37.19%	37.43%Octodon degus	–	–
Heteromyidae	2	38.73%	0.82	0.021	38.15%Dipodomys merriami	38.73%	39.31%Dipodomys spectabilis	–	–
Hystricidae	2	38.35%	0.75	0.020	37.81%Hystrix indica	38.35%	38.88%Hystrix brachyura	–	–
Echimyidae	2	35.09%	0.63	0.018	34.65%Proechimys brevicauda	35.09%	35.54%Proechimys semispinosus	–	–
Castoridae	1	41.68%	–	–	41.68%Castor canadensis	41.68%	41.68%Castor canadensis	–	–
Chinchillidae	1	40.88%	–	–	40.88%Chinchilla lanigera	40.88%	40.88%Chinchilla lanigera	–	–
Dipodidae	1	41.04%	–	–	41.04%Jaculus jaculus	41.04%	41.04%Jaculus jaculus	–	–
Spalacidae	1	38.78%	–	–	38.78%Nannospalax ehrenbergi	38.78%	38.78%Nannospalax ehrenbergi	–	–
Thryonomyidae	1	36.22%	–	–	36.22%Thryonomys swinderianus	36.22%	36.22%Thryonomys swinderianus	–	–

Codon usage

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

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

Rodentia 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.