ampliconflow
Archive records ENA PRJEB20465 SRA PRJEB20465 BioProject PRJEB20465

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

PRJEB20465 released 25 Sept 2026

PRJEB20465

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 48 released samples and 48 runs.

Samples
48
Runs
48
Collection
2014-08 to 2014-08

Linked publication

Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects

10.1111/jam.12180 · 2013 · via crossref

Linked by the enrich stage. Fields taken from the paper: . No per-sample coordinates in the paper.

Linked by the enrich stage from crossref.

Location

sampling sites from the release coordinates

No sample coordinates in this release

The study reports no latitude or longitude, and its metadata carries no lat_lon text field either, so no map or place-name hierarchy can be drawn. Every other panel is computed from the count table and the sample metadata.

How the sequences were obtained

sample to release
01 study metadata

Sample collection

48 samples, 2014-08 to 2014-08

no coordinates in the release

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

primers: present, trimmed; 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 MiSeq

48 runs; PAIRED 251.0 bp reads

07 this release

Denoising

dada2 1.38.0

5,310 ASVs from 1,517,927 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 1,517,927 reads from 48 runs, QC to 99.1% 16S identity and 91.8% above Q30, primers trimmed, dada2 1.38.0 to 5,310 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).

48

Samples

48 runs

5.3k

Features

OTUs at 97%

1.5M

Reads

mapped total

3.4 MB

Release size

128 files

Depth floor

1,000 reads

no samples below

QC warnings

3

6% of runs warned

Reads per sample

log scale
min
7,659
median
25,583
max
131,198

Feature detection

100.0% non-zero

5,310 / 5,310 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 985,401 (64.9%)
  • Bacillota 244,496 (16.1%)
  • Bacteroidota 175,310 (11.5%)
  • Thermodesulfobacteriota 43,464 (2.9%)
  • Actinomycetota 32,245 (2.1%)
  • Acidobacteriota 12,362 (0.8%)
  • Cyanobacteriota 7,679 (0.5%)
  • Planctomycetota 3,623 (0.2%)
  • Myxococcota 1,979 (0.1%)
  • Chloroflexota 1,954 (0.1%)
  • Ignavibacteriota 1,932 (0.1%)
  • Verrucomicrobiota 1,920 (0.1%)
  • Campylobacterota 1,219 (0.1%)
  • Gemmatimonadota 607 (0.0%)
  • Spirochaetota 573 (0.0%)
  • Fusobacteriota 547 (0.0%)
  • Bdellovibrionota 520 (0.0%)
  • Thermoproteota 387 (0.0%)
  • Chlamydiota 332 (0.0%)
  • Elusimicrobiota 299 (0.0%)

Top genera

  • Pseudomonas 562,458 (37.1%)
  • Incertae Sedis 117,107 (7.7%)
  • Hydrogenophaga 104,403 (6.9%)
  • Lutibacter 77,764 (5.1%)
  • Maritimimonas 77,426 (5.1%)
  • Staphylococcus 67,223 (4.4%)
  • Rhodoferax 57,655 (3.8%)
  • Desulfuromonas 35,687 (2.4%)
  • Erysipelothrix 30,351 (2.0%)
  • Acinetobacter 28,747 (1.9%)
  • Soehngenia 20,748 (1.4%)
  • Eperythrozoon 18,024 (1.2%)
  • Acidovorax 16,880 (1.1%)
  • TC1 15,882 (1.0%)
  • Thiobacillus 15,832 (1.0%)
  • Bacillus 11,210 (0.7%)
  • Methylobacterium 9,825 (0.6%)
  • Fusibacter 9,054 (0.6%)
  • Comamonas 8,288 (0.5%)
  • Thiovirga 8,235 (0.5%)

Rank-abundance

log-log
1 10 100 1k 10k 1 10 100 ASV_1 · Pseudomonas: 87804 reads ASV_2 · Lutibacter: 59261 reads ASV_3 · Pseudomonas: 44876 reads ASV_4 · Pseudomonas: 32614 reads ASV_5 · Pseudomonas: 23355 reads ASV_6 · Pseudomonas: 21473 reads ASV_7 · Pseudomonas: 20627 reads ASV_8 · Pseudomonas: 19554 reads ASV_9 · Incertae Sedis: 19550 reads ASV_10 · Rhodoferax: 16230 reads ASV_11 · Rhodoferax: 15067 reads ASV_12 · Pseudomonas: 13581 reads ASV_13 · Hydrogenophaga: 13196 reads ASV_14 · Pseudomonas: 12063 reads ASV_15 · Maritimimonas: 11275 reads ASV_16 · Pseudomonas: 10451 reads ASV_17 · Pseudomonas: 8970 reads ASV_18 · Acinetobacter: 8391 reads ASV_19 · Maritimimonas: 8186 reads ASV_20 · Pseudomonas: 7766 reads ASV_21 · Pseudomonas: 7679 reads ASV_22 · Maritimimonas: 7138 reads ASV_23 · Pseudomonas: 7035 reads ASV_24 · Maritimimonas: 6995 reads ASV_25 · Incertae Sedis: 6633 reads ASV_26 · Pseudomonas: 6582 reads ASV_27 · Soehngenia: 6406 reads ASV_28 · Pseudomonas: 5874 reads ASV_29 · Incertae Sedis: 5795 reads ASV_30 · Erysipelothrix: 5371 reads ASV_31 · Pseudomonas: 5277 reads ASV_32 · Desulfuromonas: 5192 reads ASV_33 · Maritimimonas: 5163 reads ASV_34 · Pseudomonas: 5148 reads ASV_35 · Incertae Sedis: 5122 reads ASV_36 · Thiobacillus: 5059 reads ASV_37 · Maritimimonas: 5026 reads ASV_38 · Pseudomonas: 5011 reads ASV_39 · Soehngenia: 4993 reads ASV_40 · Staphylococcus: 4749 reads ASV_41 · Pseudomonas: 4707 reads ASV_42 · Pseudomonas: 4609 reads ASV_43 · Pseudomonas: 4587 reads ASV_44 · Lutibacter: 4344 reads ASV_45 · Staphylococcus: 3995 reads ASV_46 · Pseudomonas: 3954 reads ASV_47 · Desulfuromonas: 3950 reads ASV_48 · Erysipelothrix: 3926 reads ASV_49 · TC1: 3917 reads ASV_50 · Pseudomonas: 3897 reads ASV_51 · Pseudomonas: 3818 reads ASV_52 · Pseudomonas: 3627 reads ASV_53 · Lutibacter: 3595 reads ASV_54 · Rhodoferax: 3432 reads ASV_55 · Acidovorax: 3321 reads ASV_56 · Staphylococcus: 3250 reads ASV_57 · Staphylococcus: 3246 reads ASV_58 · Staphylococcus: 3095 reads ASV_59 · Staphylococcus: 3093 reads ASV_60 · Staphylococcus: 3077 reads ASV_61 · Pseudomonas: 2967 reads ASV_62 · Pseudomonas: 2944 reads ASV_63 · Staphylococcus: 2937 reads ASV_64 · Pseudomonas: 2914 reads ASV_65 · Pseudomonas: 2766 reads ASV_66 · Desulfuromonas: 2755 reads ASV_67 · Desulfuromonas: 2656 reads ASV_68 · Incertae Sedis: 2546 reads ASV_69 · Pseudomonas: 2492 reads ASV_70 · Pseudomonas: 2481 reads ASV_71 · Thiobacillus: 2467 reads ASV_72 · Hydrogenophaga: 2464 reads ASV_73 · Acinetobacter: 2435 reads ASV_74 · Staphylococcus: 2393 reads ASV_75 · Staphylococcus: 2355 reads ASV_76 · Hydrogenophaga: 2325 reads ASV_77 · Pseudomonas: 2310 reads ASV_78 · Hydrogenophaga: 2284 reads ASV_79 · Staphylococcus: 2282 reads ASV_80 · Pseudomonas: 2276 reads ASV_81 · Staphylococcus: 2261 reads ASV_82 · Staphylococcus: 2204 reads ASV_83 · Pseudomonas: 2167 reads ASV_84 · Pseudomonas: 2147 reads ASV_85 · Staphylococcus: 2123 reads ASV_86 · Desulfuromonas: 2100 reads ASV_87 · Hydrogenophaga: 2081 reads ASV_88 · Desulfuromonas: 2080 reads ASV_89 · Pseudomonas: 2066 reads ASV_90 · Maritimimonas: 2066 reads ASV_91 · Staphylococcus: 2043 reads ASV_92 · Bacillus: 2037 reads ASV_93 · Pseudomonas: 2029 reads ASV_94 · Staphylococcus: 2024 reads ASV_95 · Staphylococcus: 1964 reads ASV_96 · Staphylococcus: 1928 reads ASV_97 · TC1: 1921 reads ASV_98 · Staphylococcus: 1917 reads ASV_99 · Hydrogenophaga: 1908 reads ASV_100 · Soehngenia: 1894 reads ASV_101 · Soehngenia: 1869 reads ASV_102 · Staphylococcus: 1857 reads ASV_103 · Incertae Sedis: 1846 reads ASV_104 · Pseudomonas: 1832 reads ASV_105 · Acinetobacter: 1818 reads ASV_106 · Staphylococcus: 1816 reads ASV_107 · Thiobacillus: 1802 reads ASV_108 · Hydrogenophaga: 1801 reads ASV_109 · Staphylococcus: 1796 reads ASV_110 · Staphylococcus: 1781 reads ASV_111 · Maritimimonas: 1753 reads ASV_112 · Sphingorhabdus: 1745 reads ASV_113 · Thiovirga: 1739 reads ASV_114 · Hydrogenophaga: 1738 reads ASV_115 · Pseudomonas: 1732 reads ASV_116 · Pseudomonas: 1728 reads ASV_117 · Pelotalea: 1716 reads ASV_118 · Pseudomonas: 1705 reads ASV_119 · Hydrogenophaga: 1683 reads ASV_120 · Incertae Sedis: 1681 reads ASV_121 · Pseudomonas: 1673 reads ASV_122 · Hydrogenophaga: 1660 reads ASV_123 · Pseudomonas: 1626 reads ASV_124 · Rhodoferax: 1618 reads ASV_125 · Incertae Sedis: 1596 reads ASV_126 · Hydrogenophaga: 1555 reads ASV_127 · Pseudomonas: 1552 reads ASV_128 · Erysipelothrix: 1549 reads ASV_129 · Staphylococcus: 1534 reads ASV_130 · Erysipelothrix: 1524 reads ASV_131 · Incertae Sedis: 1507 reads ASV_132 · Hydrogenophaga: 1497 reads ASV_133 · Hydrogenophaga: 1490 reads ASV_134 · Pseudomonas: 1471 reads ASV_135 · TC1: 1464 reads ASV_136 · Hydrogenophaga: 1453 reads ASV_137 · Soehngenia: 1449 reads ASV_138 · Hydrogenophaga: 1445 reads ASV_139 · Pseudomonas: 1440 reads ASV_140 · Hydrogenophaga: 1440 reads ASV_141 · Soehngenia: 1439 reads ASV_142 · Pseudomonas: 1437 reads ASV_143 · Pseudomonas: 1436 reads ASV_144 · Hydrogenophaga: 1436 reads ASV_145 · Methylotenera: 1434 reads ASV_146 · Staphylococcus: 1419 reads ASV_147 · Hydrogenophaga: 1411 reads ASV_148 · Desulfuromonas: 1400 reads ASV_149 · Fusibacter: 1394 reads ASV_150 · Pseudomonas: 1391 reads ASV_151 · Sphingorhabdus: 1384 reads ASV_152 · Desulfuromonas: 1383 reads ASV_153 · Incertae Sedis: 1359 reads ASV_154 · Pseudomonas: 1357 reads ASV_155 · Incertae Sedis: 1330 reads ASV_156 · Pseudomonas: 1321 reads ASV_157 · Pseudomonas: 1320 reads ASV_158 · Staphylococcus: 1320 reads ASV_159 · Hydrogenophaga: 1318 reads ASV_160 · TC1: 1307 reads ASV_161 · Pseudomonas: 1302 reads ASV_162 · Thiovirga: 1293 reads ASV_163 · Incertae Sedis: 1280 reads ASV_164 · Pseudomonas: 1273 reads ASV_165 · Pseudomonas: 1262 reads ASV_166 · Rhodoferax: 1254 reads ASV_167 · Sphingobium: 1252 reads ASV_168 · Sphingorhabdus: 1240 reads ASV_169 · Maritimimonas: 1222 reads ASV_170 · Pseudomonas: 1220 reads ASV_171 · Thiovirga: 1217 reads ASV_172 · Erysipelothrix: 1209 reads ASV_173 · Hydrogenophaga: 1208 reads ASV_174 · Pseudomonas: 1201 reads ASV_175 · Proteiniclasticum: 1201 reads ASV_176 · Pseudomonas: 1189 reads ASV_177 · Erysipelothrix: 1184 reads ASV_178 · Pseudomonas: 1177 reads ASV_179 · Pseudomonas: 1177 reads ASV_180 · Pseudomonas: 1174 reads ASV_181 · Hydrogenophaga: 1173 reads ASV_182 · Hydrogenophaga: 1171 reads ASV_183 · Bacillus: 1164 reads ASV_184 · Pseudomonas: 1151 reads ASV_185 · Incertae Sedis: 1144 reads ASV_186 · Desulfuromonas: 1140 reads ASV_187 · Hydrogenophaga: 1123 reads ASV_188 · Hydrogenophaga: 1115 reads ASV_189 · Bacillus: 1109 reads ASV_190 · Acidovorax: 1108 reads ASV_191 · Hydrogenophaga: 1100 reads ASV_192 · Rhodoferax: 1099 reads ASV_193 · Pseudomonas: 1098 reads ASV_194 · Hydrogenophaga: 1098 reads ASV_195 · Incertae Sedis: 1092 reads ASV_196 · Pseudomonas: 1089 reads ASV_197 · Pelotalea: 1086 reads ASV_198 · Rhodoferax: 1081 reads ASV_199 · Hydrogenophaga: 1075 reads ASV_200 · Hydrogenophaga: 1065 reads rank reads

5,310 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

48 samples
min
7,659
median
25,583
max
131,198

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 100k 504 0

Expected richness when 48 samples are subsampled to a common depth, resampled 31 draws. Median 101 features observed at full depth.

Depth against richness

log depth
550 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.668, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 99.1% alignment call per run
  • Q30 rate 91.8% mean Q 35.8
  • Amplicon V4 primers present
  • PhiX 0.0% control spike-in

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

Diversity

Shannon
3.24
Simpson
0.925
Evenness
0.712
Chao1
101

Median across samples. Observed richness ranges 39 to 550.

Feature prevalence

0 of 5,310 features

present in at least half of the 48 samples (0.0%). 4,711 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 48 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 · 15.6%

  • shannon 50.5%
  • evenness 48.0%
  • observed 14.9%
  • chao1 14.9%

pc2 · 5.7%

  • evenness 5.8%
  • shannon 4.2%
  • observed 0.1%
  • chao1 0.1%

pc3 · 5.1%

  • evenness 4.7%
  • shannon 3.3%
  • reads 0.6%
  • observed 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
5.8 48 samples

Median Shannon 3.242 across the release; observed richness runs 39 to 550.

Bray-Curtis dissimilarity

48 x 48, darker is closer

Sample order is the release order, 48 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 = 7 silhouette 0.339

  • state 0 4 samples
  • state 1 1 samples
  • state 2 5 samples
  • state 3 17 samples
  • state 4 3 samples
  • state 5 2 samples
  • state 6 16 samples

Clustered on the centred log-ratio of the top 200 features; 48 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.

Group difference and spread

Bray-Curtis, 999 permutations
PERMANOVA pseudo-F
n/a · p n/a
PERMDISP F
n/a · p n/a
Distance decay (Mantel r)
n/a · p n/a

    The contamination class separates the communities beyond the spread within each class (PERMANOVA) with no evidence that the spread itself differs (PERMDISP). Distance decay runs over n/a to n/a km.

    Spatial structure

    observed richness over distance

    the study's coordinates fall on a single site (no spread), so spatial autocorrelation is not defined

    Co-occurrence network

    100 nodes · 1,278 edges

    positive
    1,278
    negative
    0
    density
    0.258
    components
    5
    mean degree
    25.6

    Spearman on log1p proportions, 100 features, |r| ≥ 0.50, FDR 0.05.

    Hubs by degree

      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.

      ASV phylogeny

      0 most abundant of the tree

      No tree in this release.

      ASV panel

      no sequence file

      The representative sequences are not in this release, so length and GC cannot be drawn.

      Most abundant ASVs

      ASVphylumgenusmeanprev.
      ASV_1PseudomonadotaPseudomonas1829.333%
      ASV_2BacteroidotaLutibacter1234.633%
      ASV_3PseudomonadotaPseudomonas934.92%
      ASV_4PseudomonadotaPseudomonas679.52%
      ASV_5PseudomonadotaPseudomonas486.619%
      ASV_6PseudomonadotaPseudomonas447.44%
      ASV_7PseudomonadotaPseudomonas429.731%
      ASV_8PseudomonadotaPseudomonas407.44%
      ASV_9PseudomonadotaIncertae Sedis407.329%
      ASV_10PseudomonadotaRhodoferax338.133%
      ASV_11PseudomonadotaRhodoferax313.933%
      ASV_12PseudomonadotaPseudomonas282.94%

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      Missing or wrong data?

      Report a field that is empty or mistaken, or associate a paper with this study. No account is needed; the contact email is optional and used only to reply about this submission.

      Contribute to PRJEB20465

      Validated automatically where it can be, reviewed by a person where it cannot.

      Downloads

      8 files · sha256 in manifest

      Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJEB20465-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      48 samples
      Sample Collected group Reads Features Shannon State
      SAMEA103980914 2014-08 38,710 150 4.023 4
      SAMEA103980915 2014-08 20,933 128 4.569 0
      SAMEA103980916 2014-08 64,525 275 5.257 0
      SAMEA103980917 2014-08 21,774 42 2.07 6
      SAMEA103980918 2014-08 17,380 39 2.389 6
      SAMEA103980919 2014-08 24,145 50 2.287 6
      SAMEA103980920 2014-08 25,144 72 2.419 6
      SAMEA103980921 2014-08 14,642 61 2.181 3
      SAMEA103980922 2014-08 16,531 78 1.899 6
      SAMEA103980923 2014-08 15,464 55 2.005 6
      SAMEA103980924 2014-08 14,284 48 2.054 6
      SAMEA103980925 2014-08 24,724 56 1.827 6
      SAMEA103980926 2014-08 33,574 122 1.858 6
      SAMEA103980927 2014-08 31,704 126 1.966 6
      SAMEA103980928 2014-08 7,811 73 2.908 6
      SAMEA103980929 2014-08 31,672 165 3.137 1
      SAMEA103980930 2014-08 10,763 89 3.543 4
      SAMEA103980931 2014-08 10,260 81 3.154 3
      SAMEA103980932 2014-08 23,030 106 3.07 3
      SAMEA103980933 2014-08 30,291 207 4.827 3
      SAMEA103980934 2014-08 29,134 112 3.331 3
      SAMEA103980935 2014-08 8,257 52 2.064 6
      SAMEA103980936 2014-08 20,597 89 2.208 6
      SAMEA103980937 2014-08 56,614 102 2.116 3
      SAMEA103980938 2014-08 30,892 100 2.111 6
      SAMEA103980939 2014-08 27,446 83 2.345 6
      SAMEA103980940 2014-08 15,037 52 2.159 6
      SAMEA103980941 2014-08 7,659 49 3.003 3
      SAMEA103980942 2014-08 9,215 60 3.97 3
      SAMEA103980943 2014-08 31,232 166 4.977 2
      SAMEA103980944 2014-08 57,187 267 5.169 2
      SAMEA103980945 2014-08 31,169 134 4.447 0
      SAMEA103980946 2014-08 19,173 100 4.461 3
      SAMEA103980947 2014-08 26,023 117 4.399 0
      SAMEA103980948 2014-08 81,942 489 5.685 3
      SAMEA103980949 2014-08 111,190 550 4.83 3
      SAMEA103980950 2014-08 95,488 457 3.891 3
      SAMEA103980951 2014-08 27,452 471 5.777 3
      SAMEA103980952 2014-08 13,621 71 3.518 3
      SAMEA103980953 2014-08 28,105 102 3.643 5
      SAMEA103980954 2014-08 29,079 158 4.146 4
      SAMEA103980955 2014-08 14,340 90 3.67 3
      SAMEA103980956 2014-08 131,198 139 2.428 3
      SAMEA103980957 2014-08 36,674 80 2.319 5
      SAMEA103980958 2014-08 27,014 101 3.49 3
      SAMEA103980959 2014-08 15,805 81 4.305 2
      SAMEA103980960 2014-08 35,056 117 4.261 2
      SAMEA103980961 2014-08 23,967 199 5.242 2

      click a column head to sort