family · mtDNA statistics

Charadriidae

9 species in 5 genera. Every region of their mitochondrial genomes, side by side.

Group

species

44.8%

mean GC, whole genome

SD 0.4, range 44.4–45.7%

16,860

median genome length, bp

Range 15,933–16,940 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	9	44.81%	0.43	0.009	44.42%Charadrius vociferus	44.76%	45.73%Pluvialis squatarola	0.37	0.32
Protein-coding	9	45.40%	0.64	0.014	44.68%Anarhynchus leschenaultii	45.31%	46.76%Pluvialis squatarola	0.25	0.52
All rRNA	9	45.95%	0.49	0.011	45.15%Charadrius vociferus	45.83%	46.76%Pluvialis squatarola	0.74	0.02
All tRNA	9	41.90%	0.49	0.012	41.28%Charadrius vociferus	41.82%	42.70%Vanellus vanellus	0.43	0.25
12S rRNA	9	47.57%	0.80	0.017	46.56%Charadrius vociferus	47.25%	48.87%Pluvialis squatarola	0.61	0.08
16S rRNA	9	44.96%	0.40	0.009	44.29%Charadrius vociferus	45.02%	45.46%Pluvialis squatarola	0.71	0.03
D-loop	7	40.38%	0.91	0.022	39.56%Pluvialis squatarola	40.04%	42.31%Anarhynchus leschenaultii	0.12	0.8
ND1	9	44.77%	1.38	0.031	43.05%Anarhynchus leschenaultii	45.19%	46.93%Pluvialis squatarola	0.14	0.71
ND2	9	42.77%	0.94	0.022	41.58%Vanellus vanellus	42.73%	44.56%Thinornis dubius	−0.12	0.75
COX1	9	47.28%	0.57	0.012	46.55%Charadrius vociferus	47.32%	48.29%Pluvialis squatarola	0.16	0.67
COX2	9	45.35%	1.28	0.028	44.01%Charadrius vociferus	45.18%	47.37%Pluvialis squatarola	0.28	0.47
ATP8	9	42.95%	2.59	0.060	38.10%Charadrius vociferus	43.45%	46.43%Anarhynchus montanus	0.21	0.58
ATP6	9	45.85%	1.15	0.025	44.59%Anarhynchus montanus	45.47%	48.54%Pluvialis squatarola	0.36	0.34
COX3	9	46.15%	0.78	0.017	44.90%Thinornis dubius	46.17%	47.32%Pluvialis squatarola	0.48	0.19
ND3	9	43.63%	2.06	0.047	40.46%Anarhynchus alexandrinus	43.30%	46.44%Thinornis dubius	0.25	0.51
ND4L	9	46.61%	2.12	0.046	43.43%Charadrius vociferus	46.13%	49.49%Anarhynchus montanus	0.27	0.47
ND4	9	44.96%	1.04	0.023	43.54%Thinornis dubius	45.14%	46.30%Pluvialis squatarola	0.15	0.71
ND5	9	44.66%	0.48	0.011	44.13%Thinornis dubius	44.63%	45.56%Pluvialis squatarola	0.21	0.59
ND6	9	46.81%	1.52	0.032	44.83%Charadrius vociferus	46.36%	48.94%Pluvialis squatarola	0.28	0.47
CYTB	8	46.46%	0.91	0.020	45.23%Anarhynchus leschenaultii	46.50%	48.12%Charadrius vociferus	−0.24	0.57

Genera of Charadriidae

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

Region

Parameter

Chart

Genera of Charadriidae

Anarhynchus	4	44.62%	0.17	0.004	44.44%Anarhynchus mongolus	44.65%	44.77%Anarhynchus montanus	–	–
Pluvialis	2	45.43%	0.43	0.009	45.13%Pluvialis fulva	45.43%	45.73%Pluvialis squatarola	–	–
Vanellus	1	44.53%	–	–	44.53%Vanellus vanellus	44.53%	44.53%Vanellus vanellus	–	–
Charadrius	1	44.42%	–	–	44.42%Charadrius vociferus	44.42%	44.42%Charadrius vociferus	–	–
Thinornis	1	45.01%	–	–	45.01%Thinornis dubius	45.01%	45.01%Thinornis dubius	–	–

Codon usage

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

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

Charadriidae 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.