family · mtDNA statistics

Cichlidae

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

Group

species

46.2%

mean GC, whole genome

SD 0.5, range 45.6–47.0%

16,621

median genome length, bp

Range 16,530–16,642 bp

genera

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	8	46.15%	0.47	0.010	45.62%Oreochromis mossambicus	46.11%	46.96%Coptodon zillii	−0.54	0.17
Protein-coding	8	46.85%	0.66	0.014	46.12%Oreochromis mossambicus	46.77%	48.07%Coptodon zillii	−0.63	0.1
All rRNA	8	47.14%	0.40	0.008	46.36%Cichla temensis	47.21%	47.57%Oreochromis esculentus	0.69	0.06
All tRNA	8	44.88%	0.36	0.008	44.20%Cichla temensis	44.87%	45.36%Tropheus moorii	0.51	0.19
12S rRNA	8	49.59%	0.46	0.009	49.26%Oreochromis andersonii	49.37%	50.53%Oreochromis esculentus	0.08	0.86
16S rRNA	8	45.78%	0.55	0.012	44.71%Cichla temensis	45.95%	46.44%Oreochromis niloticus	0.76	0.03
D-loop	7	36.84%	1.99	0.054	35.24%Oreochromis andersonii	35.93%	41.01%Cichla temensis	−0.57	0.18
ND1	8	47.23%	0.92	0.019	46.46%Oreochromis andersonii	46.87%	49.13%Coptodon zillii	−0.55	0.16
ND2	8	48.03%	0.95	0.020	47.04%Tropheus moorii	47.61%	49.71%Herichthys cyanoguttatus	−0.94	4.6 × 10⁻⁴
COX1	8	46.37%	1.15	0.025	45.23%Cichla temensis	46.04%	48.93%Coptodon zillii	−0.18	0.68
COX2	8	44.92%	1.29	0.029	42.69%Tropheus moorii	44.93%	47.18%Coptodon zillii	−0.35	0.4
ATP8	8	45.09%	1.79	0.040	42.26%Cichla temensis	45.24%	47.02%Oreochromis niloticus	0.53	0.18
ATP6	8	45.93%	2.11	0.046	43.41%Oreochromis andersonii	45.54%	48.98%Coptodon zillii	−0.54	0.17
COX3	8	47.40%	0.86	0.018	46.07%Oreochromis mossambicus	47.51%	48.34%Coptodon zillii	−0.16	0.7
ND3	8	47.82%	1.87	0.039	44.99%Tropheus moorii	47.99%	51.29%Cichla temensis	−0.71	0.05
ND4L	8	51.43%	2.00	0.039	49.16%Cichla temensis	50.84%	55.89%Oreochromis esculentus	0.36	0.39
ND4	8	46.60%	0.92	0.020	45.47%Oreochromis niloticus	46.32%	48.23%Herichthys cyanoguttatus	−0.49	0.22
ND5	8	45.78%	0.85	0.018	44.58%Oreochromis mossambicus	45.83%	46.71%Herichthys cyanoguttatus	−0.47	0.24
ND6	8	48.99%	1.41	0.029	47.32%Cichla temensis	48.56%	51.72%Coptodon zillii	0.06	0.88
CYTB	8	46.98%	0.74	0.016	45.92%Oreochromis niloticus	46.79%	48.29%Tropheus moorii	−0.08	0.85

Genera of Cichlidae

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

Region

Parameter

Chart

Genera of Cichlidae

Oreochromis	4	45.88%	0.35	0.008	45.62%Oreochromis mossambicus	45.75%	46.38%Oreochromis esculentus	–	–
Herichthys	1	46.54%	–	–	46.54%Herichthys cyanoguttatus	46.54%	46.54%Herichthys cyanoguttatus	–	–
Coptodon	1	46.96%	–	–	46.96%Coptodon zillii	46.96%	46.96%Coptodon zillii	–	–
Tropheus	1	46.29%	–	–	46.29%Tropheus moorii	46.29%	46.29%Tropheus moorii	–	–
Cichla	1	45.92%	–	–	45.92%Cichla temensis	45.92%	45.92%Cichla temensis	–	–

Codon usage

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

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

Cichlidae 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.