family · mtDNA statistics

Muridae

20 species in 12 genera. Every region of their mitochondrial genomes, side by side.

Group

species

37.1%

mean GC, whole genome

SD 1.5, range 34.8–40.6%

16,302

median genome length, bp

Range 16,217–16,592 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	20	37.12%	1.51	0.041	34.80%Apodemus peninsulae	36.93%	40.61%Acomys cahirinus	0.11	0.66
Protein-coding	20	37.66%	1.79	0.048	35.10%Micaelamys namaquensis	37.38%	41.69%Acomys cahirinus	0.08	0.74
All rRNA	20	36.31%	1.24	0.034	34.18%Mus minutoides	36.15%	38.68%Acomys cahirinus	0.30	0.2
All tRNA	20	34.81%	1.03	0.030	32.82%Pseudomys chapmani	34.73%	37.33%Acomys cahirinus	0.24	0.32
12S rRNA	20	37.67%	1.45	0.039	35.22%Apodemus peninsulae	37.74%	40.86%Meriones unguiculatus	0.51	0.02
16S rRNA	20	35.49%	1.40	0.040	32.87%Mus minutoides	35.50%	38.81%Acomys cahirinus	0.11	0.65
D-loop	19	36.06%	1.40	0.039	34.03%Apodemus peninsulae	36.19%	39.48%Micromys minutus	−0.49	0.03
ND1	20	38.98%	2.35	0.060	35.60%Micaelamys namaquensis	38.64%	42.93%Acomys cahirinus	0.02	0.95
ND2	20	35.32%	2.71	0.077	30.70%Apodemus peninsulae	35.39%	41.08%Acomys cahirinus	0.11	0.65
COX1	20	39.90%	1.49	0.037	37.67%Apodemus peninsulae	39.81%	44.14%Acomys cahirinus	0.04	0.86
COX2	20	38.00%	1.93	0.051	34.94%Lemniscomys barbarus	38.45%	41.52%Acomys cahirinus	−0.07	0.77
ATP8	20	32.68%	2.42	0.074	27.94%Micaelamys namaquensis	31.86%	36.27%Acomys cahirinus	0.13	0.57
ATP6	20	36.88%	2.04	0.055	33.48%Lemniscomys barbarus	36.42%	40.82%Acomys cahirinus	−0.02	0.94
COX3	20	40.50%	1.71	0.042	38.01%Apodemus peninsulae	40.69%	44.13%Acomys cahirinus	0.17	0.48
ND3	20	35.38%	2.34	0.066	31.78%Micaelamys namaquensis	35.34%	41.38%Acomys cahirinus	0.12	0.61
ND4L	20	37.44%	2.66	0.071	32.66%Micromys minutus	36.70%	42.76%Rattus lutreola	0.21	0.37
ND4	20	36.22%	1.80	0.050	32.58%Mus minutoides	36.10%	39.19%Rattus lutreola	0.10	0.69
ND5	20	36.44%	2.07	0.057	33.00%Mus minutoides	36.53%	41.30%Acomys cahirinus	0.04	0.87
ND6	20	35.93%	2.38	0.066	31.79%Mus minutoides	35.92%	39.81%Acomys cahirinus	0.32	0.16
CYTB	20	39.77%	1.83	0.046	37.33%Lemniscomys barbarus	39.58%	44.09%Rattus fuscipes	−0.05	0.83

Genera of Muridae

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

Region

Parameter

Chart

Genera of Muridae

Rattus	4	38.68%	0.45	0.012	38.10%Rattus rattus	38.76%	39.12%Rattus lutreola	–	–
Meriones	3	37.58%	0.73	0.019	36.95%Meriones unguiculatus	37.40%	38.38%Meriones libycus	–	–
Mus	3	36.40%	1.09	0.030	35.18%Mus minutoides	36.74%	37.28%Mus spicilegus	–	–
Apodemus	2	35.62%	1.17	0.033	34.80%Apodemus peninsulae	35.62%	36.45%Apodemus sylvaticus	–	–
Acomys	1	40.61%	–	–	40.61%Acomys cahirinus	40.61%	40.61%Acomys cahirinus	–	–
Pseudomys	1	36.04%	–	–	36.04%Pseudomys chapmani	36.04%	36.04%Pseudomys chapmani	–	–
Micromys	1	37.31%	–	–	37.31%Micromys minutus	37.31%	37.31%Micromys minutus	–	–
Psammomys	1	36.90%	–	–	36.90%Psammomys obesus	36.90%	36.90%Psammomys obesus	–	–
Lemniscomys	1	35.31%	–	–	35.31%Lemniscomys barbarus	35.31%	35.31%Lemniscomys barbarus	–	–
Micaelamys	1	35.01%	–	–	35.01%Micaelamys namaquensis	35.01%	35.01%Micaelamys namaquensis	–	–
Grammomys	1	36.69%	–	–	36.69%Grammomys dolichurus	36.69%	36.69%Grammomys dolichurus	–	–
Chiropodomys	1	36.70%	–	–	36.70%Chiropodomys gliroides	36.70%	36.70%Chiropodomys gliroides	–	–

Codon usage

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

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

Muridae 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.