order · mtDNA statistics

Clupeiformes

42 species in 4 families. Every region of their mitochondrial genomes, side by side.

Group

species

46.9%

mean GC, whole genome

SD 1.8, range 42.4–50.1%

16,697

median genome length, bp

Range 16,541–17,158 bp

families

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	42	46.93%	1.84	0.039	42.36%Coilia mystus	47.25%	50.07%Sardina pilchardus	0.06	0.72
Protein-coding	42	47.22%	2.04	0.043	42.29%Coilia mystus	47.58%	50.82%Escualosa thoracata	0.06	0.69
All rRNA	42	48.67%	1.22	0.025	45.97%Coilia nasus	48.78%	51.08%Tenualosa toli	−0.04	0.82
All tRNA	42	47.49%	1.11	0.023	44.70%Coilia nasus	47.73%	49.48%Sardina pilchardus	0.20	0.21
12S rRNA	42	50.42%	0.73	0.014	48.59%Etrumeus teres	50.63%	51.37%Dorosoma cepedianum	−0.00	0.99
16S rRNA	42	47.69%	1.62	0.034	44.37%Coilia nasus	47.82%	50.92%Tenualosa toli	−0.04	0.79
D-loop	39	37.45%	7.16	0.191	0.00%Sardinella aurita	38.17%	49.53%Sardinella lemuru	−0.05	0.78
ND1	42	49.12%	2.61	0.053	41.95%Coilia mystus	49.64%	53.85%Escualosa thoracata	−0.03	0.86
ND2	42	49.69%	2.58	0.052	43.64%Coilia mystus	50.19%	54.45%Sardinella lemuru	0.07	0.67
COX1	42	46.24%	1.79	0.039	41.75%Thryssa kammalensis	46.32%	49.52%Sardinella lemuru	0.09	0.58
COX2	42	45.18%	1.69	0.037	40.52%Thryssa kammalensis	45.66%	48.19%Harengula jaguana	0.14	0.37
ATP8	42	42.56%	2.91	0.068	36.90%Thryssa kammalensis	42.26%	48.81%Sardinella gibbosa	0.03	0.86
ATP6	42	45.58%	2.34	0.051	39.82%Coilia nasus	45.87%	50.58%Escualosa thoracata	0.14	0.39
COX3	42	48.82%	1.90	0.039	44.71%Coilia mystus	49.14%	52.23%Sardina pilchardus	0.15	0.36
ND3	42	46.74%	2.52	0.054	40.29%Coilia nasus	46.86%	51.00%Nematalosa erebi	0.05	0.75
ND4L	42	49.59%	2.81	0.057	41.41%Etrumeus teres	49.66%	55.22%Escualosa thoracata	0.05	0.73
ND4	42	47.46%	2.45	0.052	41.20%Coilia mystus	47.65%	51.34%Escualosa thoracata	0.07	0.67
ND5	42	46.12%	2.30	0.050	39.81%Coilia mystus	46.27%	49.73%Escualosa thoracata	0.05	0.77
ND6	42	48.03%	2.71	0.056	42.72%Coilia nasus	48.47%	52.87%Sardinella gibbosa	−0.04	0.81
CYTB	42	46.67%	2.08	0.045	41.54%Coilia nasus	46.63%	50.83%Sardina pilchardus	0.02	0.91

Families of Clupeiformes

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

Region

Parameter

Chart

Families of Clupeiformes

Clupeidae	30	47.76%	1.17	0.024	45.29%Potamalosa richmondia	47.70%	50.07%Sardina pilchardus	−0.18	0.34
Engraulidae	10	44.89%	1.67	0.037	42.36%Coilia mystus	45.60%	47.26%Engraulis ringens	−0.37	0.29
Dussumieriidae	1	44.62%	–	–	44.62%Etrumeus teres	44.62%	44.62%Etrumeus teres	–	–
Pristigasteridae	1	44.48%	–	–	44.48%Ilisha elongata	44.48%	44.48%Ilisha elongata	–	–

Codon usage

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

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

Clupeiformes 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.