family · mtDNA statistics

Scolopacidae

24 species in 8 genera. Every region of their mitochondrial genomes, side by side.

Group

species

43.3%

mean GC, whole genome

SD 0.8, range 41.3–44.9%

16,795

median genome length, bp

Range 16,603–18,153 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	24	43.32%	0.80	0.019	41.30%Gallinago gallinago	43.30%	44.88%Arenaria melanocephala	0.17	0.42
Protein-coding	24	43.70%	0.94	0.021	41.21%Gallinago gallinago	43.80%	45.25%Arenaria melanocephala	0.23	0.29
All rRNA	24	43.76%	0.58	0.013	42.81%Tringa glareola	43.73%	44.99%Arenaria melanocephala	0.18	0.4
All tRNA	24	41.55%	0.44	0.011	40.65%Tringa ochropus	41.67%	42.31%Arenaria melanocephala	−0.18	0.39
12S rRNA	24	46.08%	0.77	0.017	44.94%Tringa glareola	45.95%	47.63%Xenus cinereus	0.14	0.52
16S rRNA	24	42.34%	0.61	0.014	41.17%Gallinago delicata	42.24%	43.45%Arenaria melanocephala	0.16	0.45
D-loop	24	41.69%	1.84	0.044	37.64%Numenius madagascariensis	42.35%	44.57%Calidris pugnax	−0.14	0.52
ND1	24	43.58%	1.28	0.029	40.39%Gallinago gallinago	43.56%	45.50%Xenus cinereus	0.24	0.26
ND2	24	41.22%	1.61	0.039	35.60%Gallinago gallinago	41.43%	42.93%Xenus cinereus	0.06	0.78
COX1	24	45.16%	1.03	0.023	42.75%Gallinago delicata	45.13%	46.81%Numenius madagascariensis	0.03	0.9
COX2	24	44.34%	1.29	0.029	41.81%Gallinago gallinago	44.37%	47.08%Tringa brevipes	−0.27	0.2
ATP8	24	40.25%	1.60	0.040	37.50%Tringa brevipes	39.88%	43.45%Limosa lapponica	0.36	0.08
ATP6	24	45.80%	1.33	0.029	42.11%Gallinago gallinago	46.05%	47.37%Tringa melanoleuca	−0.04	0.84
COX3	24	44.61%	0.87	0.019	43.24%Tringa brevipes	44.39%	46.56%Arenaria interpres	0.11	0.6
ND3	24	43.52%	1.38	0.032	41.03%Limosa lapponica	43.16%	45.58%Arenaria interpres	0.06	0.78
ND4L	24	43.35%	2.03	0.047	39.73%Tringa brevipes	43.51%	46.80%Xenus cinereus	0.25	0.25
ND4	24	42.80%	1.21	0.028	40.13%Gallinago gallinago	42.74%	45.21%Arenaria interpres	0.35	0.09
ND5	24	42.74%	1.06	0.025	40.11%Gallinago gallinago	42.86%	44.13%Calidris ruficollis	0.35	0.09
ND6	24	43.60%	1.21	0.028	41.57%Gallinago delicata	43.58%	45.98%Xenus cinereus	0.20	0.34
CYTB	24	44.89%	1.10	0.024	43.22%Gallinago gallinago	45.10%	46.72%Arenaria melanocephala	0.41	0.05

Genera of Scolopacidae

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

Region

Parameter

Chart

Genera of Scolopacidae

Tringa	10	43.11%	0.26	0.006	42.67%Tringa glareola	43.06%	43.53%Tringa semipalmata	−0.09	0.8
Calidris	5	43.63%	0.29	0.007	43.34%Calidris ruficollis	43.59%	44.10%Calidris tenuirostris	−0.06	0.92
Arenaria	2	44.77%	0.16	0.004	44.66%Arenaria interpres	44.77%	44.88%Arenaria melanocephala	–	–
Gallinago	2	41.42%	0.17	0.004	41.30%Gallinago gallinago	41.42%	41.54%Gallinago delicata	–	–
Numenius	2	43.41%	0.35	0.008	43.16%Numenius madagascariensis	43.41%	43.65%Numenius phaeopus	–	–
Scolopax	1	43.19%	–	–	43.19%Scolopax rusticola	43.19%	43.19%Scolopax rusticola	–	–
Limosa	1	43.70%	–	–	43.70%Limosa lapponica	43.70%	43.70%Limosa lapponica	–	–
Xenus	1	44.44%	–	–	44.44%Xenus cinereus	44.44%	44.44%Xenus cinereus	–	–

Codon usage

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

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

Scolopacidae 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.