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Table 1 Descriptions of variables used in simulation equations

From: Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Variable

Description

G + C

Proportion of DNA that is guanine or cytosine

ρt

Theoretical BD of a fragment based on fragment G + C

ρ

BD of fragment after accounting for isotopic labeling

σ

Standard deviation of fragment BD (ρ)

ρmin

Minimum BD of window to be sequenced

ρmax

Maximum BD of window to be sequenced

ρDBLmin

Minimum BD of the DBL for a fragment

ρDBLmin

Maximum BD of the DBL for a fragment

A

Atom % excess of the fragment

δ

Increase in DNA BD if atom % excess is 100% (13C: 0.036, 15N: 0.016)

pDBL

Proportion of DNA found in the diffusive boundary layer. 1 − pDBL is the proportion of DNA found in the lumen of the tube

pLR

Proportion of the fragment lumen population recovered in the BD window

rt

Radius of the ultracentrifuge tube

rmin

Minimum distance from the axis of rotation to the tube

rmax

Maximum distance from the axis of rotation to the tube

x

Fragment distance from the axis of rotation at equilibrium

xmin

Minimum position on tube of the DBL range for a fragment

xmax

Maximum position on tube of the DBL range for a fragment

α

Abundance of the genome/fragment in the sample

αL

Abundance of the fragment in the lumen of the tube within the BD

αDBL

Abundance of a fragment in the DBL within the BD window

αf

Abundance of the fragment in the BD window

αr

Abundance of reads from the fragment

l

Length of the fragment in base pairs

lr

Read length in base pairs

R

Universal gas constant (8.314 J/molK)

T

Temperature in kelvin

β

Proportionality constant of aqueous cesium chloride (1.14 × 109)

G

Buoyancy factor (7.87 × 10−10)

Mc

Mean molar weight of standard nucleotide base pair in cesium chloride solution (882)

D

Average density of the gradient solution

ω

Angular velocity of centrifugation

I

Isoconcentration point

θ

Angle of the tube relative to the axis of rotation in radians