ampliconflow
Archive records ENA PRJNA945462 SRA PRJNA945462 BioProject PRJNA945462

opens the authoritative record at ENA, SRA or BioSample; this page never replaces it

PRJNA945462 released 25 Sept 2026

PRJNA945462

Pipeline 0.1.0 Contract v0.1 Licence CC-BY-4.0

Tags

derived from the release metadata, not hand-written

Study

The study record carries no description, and its registered title is the accession itself. The figures below are computed from the 2 released samples and 2 runs.

Samples
2
Runs
2
Collection
2021-07 to 2021-07

Linked publication

No publication linked for this study.

Location

sampling sites from the release coordinates
2sampling sites · drag to pan, scroll or pinch to zoom

Place name hierarchy

  1. ▸ United States
  2. › New Hampshire
  3. › Rockingham County

Districts named on the samples

  • Rockingham County 1

Latitude 43.04181 to 43.04181, longitude -70.71524 to -70.71524. Names resolved with OpenStreetMap Nominatim from the release's own coordinates; Coordinates parsed from the released lat_lon text field, which the pipeline keeps but does not split into latitude/longitude columns.

How the sequences were obtained

sample to release
01 study metadata

Sample collection

2 samples, 2021-07 to 2021-07

43.0418 to 43.0418 N, -70.7152 to -70.7152 E

02 not reported

Storage

not reported

neither the archive nor the linked paper states storage conditions

03 not reported

Processing

not reported

no extraction kit or lysis protocol in the archive or the linked paper

04 per-run QC

PCR

16S rRNA V4-V5

primers: present; polymerase, cycle count and primer sequences are not stated in the linked paper

05 not reported

Sequencing preparation

not reported

no library kit or index strategy in the archive or the linked paper

06 study metadata

Sequencing

Illumina HiSeq 2500

2 runs; SINGLE 251.0 bp reads

07 this release

Denoising

dada2 1.38.0

50 ASVs from 96,363 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 96,363 reads from 2 runs, QC to 99.0% 16S identity and 91.7% above Q30, primers trimmed, dada2 1.38.0 to 50 ASVs, taxonomy against a SINTAX reference, then the release (CC-BY-4.0).

Steps 1 to 6 are how the sequences were obtained, from the study's own archive metadata. Step 7 is what the authors report doing with the sequences in the linked paper. ampliconflow starts at the deposited reads rather than repeating the wet lab.

Taxonomy assigned with SILVA 138.2 (SINTAX).

2

Samples

2 runs

50

Features

OTUs at 97%

96.4k

Reads

mapped total

99 MB

Release size

36 files

Depth floor

1,000 reads

no samples below

Reads per sample

log scale
min
6,537
median
48,181
max
89,826

Feature detection

100.0% non-zero

50 / 50 features

Features with at least one observed read. The remainder are present in the reference set but not detected in these samples.

Composition

Top phyla

  • Pseudomonadota 89,843 (93.2%)
  • Actinomycetota 6,520 (6.8%)

Top genera

  • Achromobacter 89,824 (93.2%)
  • Microbacterium 6,520 (6.8%)
  • Massilia 17 (0.0%)
  • Roseomonas 2 (0.0%)

Rank-abundance

log-log
1 10 100 1k 1 10 ASV_1 · Achromobacter: 6662 reads ASV_2 · Achromobacter: 5475 reads ASV_3 · Achromobacter: 5193 reads ASV_4 · Achromobacter: 4933 reads ASV_5 · Achromobacter: 4632 reads ASV_6 · Achromobacter: 4588 reads ASV_7 · Achromobacter: 4180 reads ASV_8 · Achromobacter: 4132 reads ASV_9 · Achromobacter: 3832 reads ASV_10 · Achromobacter: 3766 reads ASV_11 · Achromobacter: 3757 reads ASV_12 · Achromobacter: 3667 reads ASV_13 · Achromobacter: 3353 reads ASV_14 · Achromobacter: 3263 reads ASV_15 · Achromobacter: 3173 reads ASV_16 · Achromobacter: 3095 reads ASV_17 · Achromobacter: 3072 reads ASV_18 · Achromobacter: 3025 reads ASV_19 · Achromobacter: 2975 reads ASV_20 · Achromobacter: 2725 reads ASV_21 · Achromobacter: 2647 reads ASV_22 · Achromobacter: 2570 reads ASV_23 · Achromobacter: 2569 reads ASV_24 · Achromobacter: 2531 reads ASV_25 · Microbacterium: 529 reads ASV_26 · Microbacterium: 438 reads ASV_27 · Microbacterium: 432 reads ASV_28 · Microbacterium: 380 reads ASV_29 · Microbacterium: 364 reads ASV_30 · Microbacterium: 351 reads ASV_31 · Microbacterium: 330 reads ASV_32 · Microbacterium: 321 reads ASV_33 · Microbacterium: 314 reads ASV_34 · Microbacterium: 312 reads ASV_35 · Microbacterium: 298 reads ASV_36 · Microbacterium: 288 reads ASV_37 · Microbacterium: 278 reads ASV_38 · Microbacterium: 277 reads ASV_39 · Microbacterium: 275 reads ASV_40 · Microbacterium: 265 reads ASV_41 · Microbacterium: 251 reads ASV_42 · Microbacterium: 227 reads ASV_43 · Microbacterium: 218 reads ASV_44 · Microbacterium: 193 reads ASV_45 · Microbacterium: 179 reads ASV_46 · Massilia: 12 reads ASV_47 · Achromobacter: 6 reads ASV_48 · Massilia: 5 reads ASV_49 · Achromobacter: 3 reads ASV_50 · Roseomonas: 2 reads rank reads

50 ranked features. A steep drop means a few taxa carry most of the reads.

Per-sample reads

2 samples
min
6,537
median
48,181
max
89,826

Downstream QC and analysis

computed from the released tables

Eleven modules, computed from the released count table, the sample metadata and the per-run QC reports. Each panel states its own n and the test it used; a module that cannot run on this release is shown as a flagged gap rather than an empty frame.

Rarefaction

median with p10 to p90
2k 5k 10k 20k 50k 26 0

Expected richness when 2 samples are subsampled to a common depth, resampled 31 draws. Median 25 features observed at full depth.

Depth against richness

log depth
26 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is , so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 99.0% alignment call per run
  • Q30 rate 91.7% mean Q 35.6
  • Amplicon V4-V5 primers present
  • PhiX 0.0% control spike-in

2 run report(s), n/a GC, 0.0% ambiguous bases.

Diversity

Shannon
3.08
Simpson
0.952
Evenness
0.958
Chao1
25

Median across samples. Observed richness ranges 24 to 26.

Feature prevalence

50 of 50 features

present in at least half of the 2 samples (100.0%). 50 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 2 plotted. Choose the axes and the colour variable; hover a point for its sample id. The legend below the axes names the levels or the numeric range.

What explains each axis

pc1 · 100.0%

pc2 · 0.0%

pc3 · 0.0%

Categorical variables use eta-squared (between-group share of the axis), numeric ones the squared Pearson correlation. Computed from the released sample metadata.

Alpha diversity per sample

Shannon
3.1 2 samples

Median Shannon 3.082 across the release; observed richness runs 24 to 26.

Bray-Curtis dissimilarity

2 x 2, darker is closer

Sample order is the release order, 2 labels, and the matrix itself ships as beta_distance.tsv beside the analysis.

Phylogenetic diversity

Not available for this release: no Newick tree beside the table; run the tree stage, then re-run analyze. The legacy analysis computed Faith's PD when the container carried a tree, and this one reports the absence instead of an empty column.

Community states

CLR, k by silhouette

k = n/a silhouette n/a

Clustered on the centred log-ratio of the top 200 features; samples.

Batch-bias audit

states against

adjusted Rand n/a p = n/a

not enough levels to test

permutations. Every sample here carries both MiSeq and MiniSeq runs, so the batch variable used is the one with two levels, here .

Variance partitioning

mean R2 per feature, CLR

Joint R2 n/a, so the metadata explains a modest slice of the feature variation, and the two variables are not independent of one another.

Effect size

No two-level comparison available.

Taxa against all samples

with

features tested, 0 survive the correction at q ≤ 0.05

Nothing survives. The smallest q is n/a, which is the honest answer for a study whose samples are spread across three years with two to thirteen samples per year.

Phylogenetic and signal analyses need a tree

no Newick tree beside the table; run the tree stage, then re-run analyze. The tree stage aligns the ASVs with MAFFT and builds with FastTree, both detected as external tools; neither is installed on the machine this page was built on, so Faith's PD, UniFrac, Pagel's lambda and Blomberg's K are left flagged rather than guessed.

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Ranked from the released tables: genus composition as Bray-Curtis similarity, shared environment and method terms, the distance between sample centroids, and authors shared with the linked publication.

Missing or wrong data?

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Contribute to PRJNA945462

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Downloads

8 files · sha256 in manifest

Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJNA945462-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

Samples

2 samples
Sample Collected group Reads Features Shannon State
SAMN33785634 2021-07-28 89,826 26 3.143
SAMN33785635 2021-07-28 6,537 24 3.022

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