Powell lettuce phyllosphere
Read pairs per library
What each library is made of
Top genera across all leaf samples
Microbial domains per source
Click a wedge to zoom in. Click the centre or a name in the trail above to zoom out. Wedge size is the share of read pairs.
Compare two samples or groups
Click a wedge in either chart to zoom both to the same taxon; click the centre to zoom out. Hover shows both samples.
Fold change
x: average share in A and B. y: log2(B ÷ A), with half a read added to both so taxa missing from one side can be drawn.
Scatter
Each dot is one taxon. Lines: equal, 2× and 10×. Orange: found in only one of the two.
Composition
Biggest changes
Chart builder
Ordination builder
Rank-abundance
Shared and unique taxa across treatments
Detection vs sequencing depth
Which taxa rise and fall together?
Spearman correlation of relative abundance across the leaf samples with ≥1,000 read pairs. Blue = rise together, red = opposite.
Data table
What each sample is made of
Share of read pairs in each group. Samples run unwashed → wash 1 → wash 2 within each source.
Does washing remove microbes?
Microbial read pairs (bacteria, archaea, fungi, protists, viruses) per 1,000 lettuce read pairs. Lettuce DNA is the yardstick for how much leaf went into each library, so this corrects for sample size. Dots are replicates A and B; the bar is their mean.
Percent of the chosen reads in each sample. Click a taxon to open it in the explorer and see it in every sample.
How diverse is each sample?
Have we seen everything? Rarefaction
Each curve re-counts the names found as fewer and fewer reads are kept. A curve still climbing at the right means more sequencing would find more names. Hover a curve to pick it out.
Which samples look alike?
Samples placed so that similar microbial communities (by genus, Bray–Curtis) sit close together. Only samples with at least 1,000 genus-assigned reads. Click a point to open that sample.
Similarity matrix
Darker = more of the community shared. The tree on top groups the most similar samples first.
Change per lettuce read after wash 1 (filled) and wash 2 (open), replicates pooled, for the 30 most common genera on unwashed leaves. Orange lines: all microbes together.
Checking the main organisms against whole genomes
Non-lettuce reads aligned to panels of reference genomes for each group. Click a row for the closest genomes.
Assembling the non-lettuce reads
MEGAHIT co-assembly of the non-lettuce reads from each source.
What kind of lettuce is it?
Lettuce reads compared with 514 genotyped lettuce accessions (Simko et al. 2023) at the panel positions they cover.
Lettuce types, mapped
Principal components of the 514-accession panel; each star is one source, placed by its covered positions.
Mismatch with each type
Share of covered positions where the reads disagree with the 3 closest accessions of each type. Lower = closer.
Panel test
Panel accessions, cut down to the same number of positions and called the same way.
Trait genes: did any read land on a causal site?
eIF4E (lettuce mosaic virus resistance) and red-leaf genes RLL1–RLL5. Click a gene to see its reads.
Nearest accessions
How far from Salinas?
Base differences per 1,000 aligned bases against the Salinas reference genome (includes sequencing errors, so compare samples rather than reading the number alone).
Lettuce reads per 1-Mb window on the nine chromosomes, relative to the average window. Gaps are repeats where reads cannot be placed confidently.
Read depth along the Salinas organelle genome for each source, and every position where a source's reads disagree with Salinas.
Gene screen
Reads, quality and controls
Read quality, cycle by cycle
Unassigned reads and barcode cross-talk
Comparing with BaseSpace DRAGEN Metagenomics
Same organism, two pipelines
Each dot is one taxon. Across: read pairs on this page. Up: read pairs DRAGEN assigned. Dots on the dashed line agree; dots far above it were reported mostly by DRAGEN, far below mostly here. Click a dot to look at it.
One taxon, sample by sample
Read pairs per sample from each pipeline. Taxa marked ★ had their reads looked at one by one.
DRAGEN's organism panel
The fixed list of organisms the DRAGEN app reports on, with its status and read count for each sample.