ampliconflow
Archive records ENA PRJNA666233 SRA PRJNA666233 BioProject PRJNA666233

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

PRJNA666233 released 25 Sept 2026

PRJNA666233

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 23 released samples and 23 runs.

Samples
23
Runs
23
Collection
2018-06 to 2018-06

Linked publication

No publication linked for this study.

Location

sampling sites from the release coordinates
23sampling sites · drag to pan, scroll or pinch to zoom

Place name hierarchy

  1. ▸ 中国
  2. › 湖南省
  3. › 石门县

Districts named on the samples

  • 石门县 1

Latitude 29.58 to 29.58, longitude 111.38 to 111.6. 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

23 samples, 2018-06 to 2018-06

29.5800 to 29.5800 N, 111.3800 to 111.6000 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

primers: 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 HiSeq 2500

23 runs; SINGLE 253.0 bp reads

07 this release

Denoising

dada2 1.38.0

13,732 ASVs from 1,147,931 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 1,147,931 reads from 23 runs, QC to 96.4% 16S identity and 50.8% above Q30, primers trimmed, dada2 1.38.0 to 13,732 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).

23

Samples

23 runs

13.7k

Features

OTUs at 97%

1.1M

Reads

mapped total

132 MB

Release size

78 files

Depth floor

1,000 reads

no samples below

QC warnings

23

100% of runs warned

Reads per sample

log scale
min
41,928
median
49,805
max
62,479

Feature detection

100.0% non-zero

13,732 / 13,732 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

  • Actinomycetota 261,366 (22.8%)
  • Pseudomonadota 212,718 (18.5%)
  • Acidobacteriota 194,491 (16.9%)
  • Chloroflexota 111,315 (9.7%)
  • Bacillota 71,077 (6.2%)
  • Bacteroidota 58,717 (5.1%)
  • Gemmatimonadota 49,286 (4.3%)
  • Cyanobacteriota 44,193 (3.8%)
  • Myxococcota 39,944 (3.5%)
  • Planctomycetota 23,107 (2.0%)
  • Verrucomicrobiota 21,272 (1.9%)
  • Candidatus Eremiobacterota 11,464 (1.0%)
  • Armatimonadota 9,925 (0.9%)
  • Patescibacteria 8,386 (0.7%)
  • RCP2-54 5,042 (0.4%)
  • Thermodesulfobacteriota 4,601 (0.4%)
  • Thermoproteota 4,385 (0.4%)
  • Bdellovibrionota 3,196 (0.3%)
  • GAL15 1,675 (0.1%)
  • Nitrospirota 1,547 (0.1%)

Top genera

  • Incertae Sedis 513,112 (44.7%)
  • Nocardioides 29,618 (2.6%)
  • Sphingomonas 27,989 (2.4%)
  • Candidatus Solibacter 26,871 (2.3%)
  • Bryobacter 22,797 (2.0%)
  • Acidothermus 22,004 (1.9%)
  • Peribacillus 17,258 (1.5%)
  • WCHB1-32 16,158 (1.4%)
  • Gemmatimonas 16,122 (1.4%)
  • Acidiferrimicrobium 14,699 (1.3%)
  • Ellin6067 10,403 (0.9%)
  • Marmoricola 9,417 (0.8%)
  • Conexibacter 8,689 (0.8%)
  • Acidibacter 8,171 (0.7%)
  • Corallococcus 8,047 (0.7%)
  • 1921-2 7,720 (0.7%)
  • Bradyrhizobium 7,236 (0.6%)
  • Terrabacter 6,976 (0.6%)
  • Anaerolinea 6,836 (0.6%)
  • Flavisolibacter 6,391 (0.6%)

Rank-abundance

log-log
1 10 100 1k 10k 1 10 100 ASV_1 · Incertae Sedis: 11101 reads ASV_2 · Marmoricola: 7927 reads ASV_3 · Nocardioides: 7077 reads ASV_4 · Corallococcus: 6793 reads ASV_5 · Candidatus Solibacter: 6404 reads ASV_6 · Incertae Sedis: 5602 reads ASV_7 · Terrabacter: 5381 reads ASV_8 · WCHB1-32: 5254 reads ASV_9 · Peribacillus: 5139 reads ASV_10 · Sphingomonas: 4760 reads ASV_11 · Lactobacillus: 4597 reads ASV_12 · Pedococcus-Phycicoccus: 4274 reads ASV_13 · Angustibacter: 4145 reads ASV_14 · Pseudarthrobacter: 4012 reads ASV_15 · Nocardioides: 3851 reads ASV_16 · Peribacillus: 3760 reads ASV_17 · WCHB1-32: 3353 reads ASV_18 · Incertae Sedis: 3112 reads ASV_19 · Incertae Sedis: 2805 reads ASV_20 · Schinkia: 2727 reads ASV_21 · Incertae Sedis: 2723 reads ASV_22 · Ellin6067: 2713 reads ASV_23 · Incertae Sedis: 2678 reads ASV_24 · Incertae Sedis: 2677 reads ASV_25 · Peribacillus: 2654 reads ASV_26 · Acidothermus: 2638 reads ASV_27 · Incertae Sedis: 2578 reads ASV_28 · WCHB1-32: 2510 reads ASV_29 · Incertae Sedis: 2500 reads ASV_30 · Bradyrhizobium: 2484 reads ASV_31 · Janibacter: 2432 reads ASV_32 · Incertae Sedis: 2419 reads ASV_33 · Incertae Sedis: 2414 reads ASV_34 · Incertae Sedis: 2320 reads ASV_35 · Intrasporangium: 2306 reads ASV_36 · Incertae Sedis: 2218 reads ASV_37 · Incertae Sedis: 2208 reads ASV_38 · Incertae Sedis: 2164 reads ASV_39 · Desulfovirga: 2158 reads ASV_40 · Incertae Sedis: 2151 reads ASV_41 · Incertae Sedis: 2144 reads ASV_42 · Bradyrhizobium: 2140 reads ASV_43 · Tetrasphaera: 2131 reads ASV_44 · WCHB1-32: 2122 reads ASV_45 · Incertae Sedis: 2104 reads ASV_46 · Incertae Sedis: 2074 reads ASV_47 · Incertae Sedis: 2058 reads ASV_48 · Gemmatimonas: 1991 reads ASV_49 · Occallatibacter: 1973 reads ASV_50 · Nocardioides: 1936 reads ASV_51 · Acidothermus: 1924 reads ASV_52 · Blastococcus: 1905 reads ASV_53 · Peribacillus: 1879 reads ASV_54 · Incertae Sedis: 1868 reads ASV_55 · Bryobacter: 1866 reads ASV_56 · Ellin6067: 1843 reads ASV_57 · Acidothermus: 1775 reads ASV_58 · Microcoleus SAG 1449-1a: 1739 reads ASV_59 · Incertae Sedis: 1719 reads ASV_60 · Lysinibacillus: 1698 reads ASV_61 · Incertae Sedis: 1685 reads ASV_62 · Peribacillus: 1677 reads ASV_63 · Incertae Sedis: 1664 reads ASV_64 · Sphingomonas: 1652 reads ASV_65 · Incertae Sedis: 1604 reads ASV_66 · Dongia: 1591 reads ASV_67 · Microvirga: 1568 reads ASV_68 · Incertae Sedis: 1559 reads ASV_69 · Incertae Sedis: 1555 reads ASV_70 · Incertae Sedis: 1533 reads ASV_71 · Microcoleus SAG 1449-1a: 1531 reads ASV_72 · Incertae Sedis: 1521 reads ASV_73 · Incertae Sedis: 1517 reads ASV_74 · Incertae Sedis: 1517 reads ASV_75 · Ellin6067: 1498 reads ASV_76 · Bradyrhizobium: 1486 reads ASV_77 · Incertae Sedis: 1463 reads ASV_78 · Incertae Sedis: 1413 reads ASV_79 · Incertae Sedis: 1407 reads ASV_80 · Sphingomonas: 1399 reads ASV_81 · Conexibacter: 1372 reads ASV_82 · Incertae Sedis: 1361 reads ASV_83 · Ramlibacter: 1357 reads ASV_84 · Nocardioides: 1353 reads ASV_85 · Incertae Sedis: 1351 reads ASV_86 · Modestobacter: 1349 reads ASV_87 · Rubellimicrobium: 1344 reads ASV_88 · Nostoc PCC-73102: 1323 reads ASV_89 · Sphingomonas: 1319 reads ASV_90 · Acidothermus: 1311 reads ASV_91 · Incertae Sedis: 1306 reads ASV_92 · Incertae Sedis: 1291 reads ASV_93 · Tychonema CCAP 1459-11B: 1257 reads ASV_94 · Incertae Sedis: 1246 reads ASV_95 · Candidatus Solibacter: 1242 reads ASV_96 · Dyella: 1240 reads ASV_97 · 1921-2: 1233 reads ASV_98 · Peribacillus: 1227 reads ASV_99 · Terracidiphilus: 1210 reads ASV_100 · Lentzea: 1206 reads ASV_101 · Acidiferrimicrobium: 1205 reads ASV_102 · Incertae Sedis: 1181 reads ASV_103 · Incertae Sedis: 1177 reads ASV_104 · Incertae Sedis: 1177 reads ASV_105 · Nocardioides: 1175 reads ASV_106 · Incertae Sedis: 1175 reads ASV_107 · Nakamurella: 1173 reads ASV_108 · Incertae Sedis: 1139 reads ASV_109 · Incertae Sedis: 1138 reads ASV_110 · Incertae Sedis: 1130 reads ASV_111 · Incertae Sedis: 1129 reads ASV_112 · Incertae Sedis: 1127 reads ASV_113 · Incertae Sedis: 1112 reads ASV_114 · Incertae Sedis: 1080 reads ASV_115 · Incertae Sedis: 1078 reads ASV_116 · Incertae Sedis: 1073 reads ASV_117 · Nocardioides: 1048 reads ASV_118 · Pedobacter: 1046 reads ASV_119 · Nocardioides: 1039 reads ASV_120 · Incertae Sedis: 1039 reads ASV_121 · Gaiella: 1039 reads ASV_122 · Nostoc PCC-7107: 1038 reads ASV_123 · Incertae Sedis: 1036 reads ASV_124 · Incertae Sedis: 1031 reads ASV_125 · Incertae Sedis: 1031 reads ASV_126 · Incertae Sedis: 1028 reads ASV_127 · Nocardioides: 1017 reads ASV_128 · Incertae Sedis: 1016 reads ASV_129 · Incertae Sedis: 1012 reads ASV_130 · Incertae Sedis: 1011 reads ASV_131 · Terrabacter: 999 reads ASV_132 · Phormidium IAM M-71: 998 reads ASV_133 · WCHB1-32: 996 reads ASV_134 · Incertae Sedis: 992 reads ASV_135 · Incertae Sedis: 990 reads ASV_136 · Streptomyces: 985 reads ASV_137 · Incertae Sedis: 980 reads ASV_138 · Incertae Sedis: 978 reads ASV_139 · Incertae Sedis: 974 reads ASV_140 · Incertae Sedis: 972 reads ASV_141 · Cellulomonas: 971 reads ASV_142 · Incertae Sedis: 962 reads ASV_143 · Incertae Sedis: 955 reads ASV_144 · Incertae Sedis: 951 reads ASV_145 · Incertae Sedis: 943 reads ASV_146 · FFCH7168: 942 reads ASV_147 · Incertae Sedis: 939 reads ASV_148 · Incertae Sedis: 935 reads ASV_149 · WCHB1-32: 934 reads ASV_150 · Jatrophihabitans: 933 reads ASV_151 · Bryobacter: 927 reads ASV_152 · Incertae Sedis: 927 reads ASV_153 · Candidatus Solibacter: 911 reads ASV_154 · Ramlibacter: 910 reads ASV_155 · Sphingomonas: 910 reads ASV_156 · Phenylobacterium: 908 reads ASV_157 · Nocardioides: 908 reads ASV_158 · Incertae Sedis: 907 reads ASV_159 · Incertae Sedis: 905 reads ASV_160 · Acidibacter: 902 reads ASV_161 · Rubellimicrobium: 902 reads ASV_162 · Incertae Sedis: 901 reads ASV_163 · Incertae Sedis: 901 reads ASV_164 · Incertae Sedis: 899 reads ASV_165 · Nocardioides: 895 reads ASV_166 · Gaiella: 892 reads ASV_167 · Incertae Sedis: 889 reads ASV_168 · Gracilibacter: 889 reads ASV_169 · Incertae Sedis: 888 reads ASV_170 · Incertae Sedis: 887 reads ASV_171 · Occallatibacter: 881 reads ASV_172 · Incertae Sedis: 880 reads ASV_173 · Flavisolibacter: 876 reads ASV_174 · Incertae Sedis: 876 reads ASV_175 · Gemmatimonas: 868 reads ASV_176 · Aridibacter: 867 reads ASV_177 · Solirubrobacter: 866 reads ASV_178 · Candidatus Solibacter: 866 reads ASV_179 · Acidothermus: 861 reads ASV_180 · Streptomyces: 855 reads ASV_181 · Microcella: 851 reads ASV_182 · Incertae Sedis: 835 reads ASV_183 · Anaerolinea: 833 reads ASV_184 · Incertae Sedis: 831 reads ASV_185 · Incertae Sedis: 831 reads ASV_186 · Actinoplanes: 821 reads ASV_187 · Acidothermus: 809 reads ASV_188 · Incertae Sedis: 805 reads ASV_189 · Nocardioides: 803 reads ASV_190 · Incertae Sedis: 797 reads ASV_191 · Incertae Sedis: 794 reads ASV_192 · Symplocastrum CPER-KK1: 793 reads ASV_193 · Incertae Sedis: 786 reads ASV_194 · Incertae Sedis: 780 reads ASV_195 · Crossiella: 778 reads ASV_196 · Rubrobacter: 774 reads ASV_197 · Incertae Sedis: 774 reads ASV_198 · Ramlibacter: 773 reads ASV_199 · Parasegetibacter: 767 reads ASV_200 · Ideonella: 766 reads rank reads

13,732 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

23 samples
min
41,928
median
49,805
max
62,479

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 1,375 0

Expected richness when 23 samples are subsampled to a common depth, resampled 31 draws. Median 974 features observed at full depth.

Depth against richness

log depth
1,847 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.004, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 96.4% alignment call per run
  • Q30 rate 50.8% mean Q 27.8
  • Amplicon V4 primers trimmed
  • PhiX 0.0% control spike-in

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

Diversity

Shannon
6.08
Simpson
0.995
Evenness
0.89
Chao1
974

Median across samples. Observed richness ranges 602 to 1,847.

Feature prevalence

30 of 13,732 features

present in at least half of the 23 samples (0.2%). 9,295 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 23 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 · 19.0%

  • observed 33.0%
  • chao1 33.0%
  • shannon 26.5%
  • evenness 18.9%

pc2 · 15.0%

  • evenness 4.0%
  • shannon 3.3%
  • reads 1.3%
  • observed 0.8%

pc3 · 10.0%

  • shannon 34.9%
  • evenness 31.1%
  • observed 30.6%
  • chao1 30.6%

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
6.9 23 samples

Median Shannon 6.081 across the release; observed richness runs 602 to 1847.

Bray-Curtis dissimilarity

23 x 23, darker is closer

Sample order is the release order, 23 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 = 6 silhouette 0.391

  • state 0 2 samples
  • state 1 3 samples
  • state 2 5 samples
  • state 3 2 samples
  • state 4 8 samples
  • state 5 3 samples

Clustered on the centred log-ratio of the top 200 features; 23 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 · 2,552 edges

    positive
    2,545
    negative
    7
    density
    0.516
    components
    1
    mean degree
    51.0

    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_1AcidobacteriotaIncertae Sedis482.613%
      ASV_2ActinomycetotaMarmoricola344.639%
      ASV_3ActinomycetotaNocardioides307.756%
      ASV_4MyxococcotaCorallococcus295.470%
      ASV_5AcidobacteriotaCandidatus Solibacter278.413%
      ASV_6AcidobacteriotaIncertae Sedis243.674%
      ASV_7ActinomycetotaTerrabacter234.048%
      ASV_8BacteroidotaWCHB1-32228.44%
      ASV_9BacillotaPeribacillus223.44%
      ASV_10PseudomonadotaSphingomonas207.070%
      ASV_11BacillotaLactobacillus199.956%
      ASV_12ActinomycetotaPedococcus-Phycicoccus185.822%

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      31 samples

      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?

      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 PRJNA666233

      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/PRJNA666233-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      23 samples
      Sample Collected group Reads Features Shannon State
      SAMN16294718 2018-06 49,805 1,014 6.161 4
      SAMN16294719 2018-06 49,986 1,073 6.221 4
      SAMN16294720 2018-06 50,635 1,334 6.524 3
      SAMN16294721 2018-06 43,371 1,557 6.832 4
      SAMN16294722 2018-06 62,479 1,847 6.949 4
      SAMN16294723 2018-06 42,135 902 6.081 4
      SAMN16294724 2018-06 52,493 1,046 6.034 4
      SAMN16294725 2018-06 54,928 719 5.371 0
      SAMN16294726 2018-06 50,008 701 5.35 0
      SAMN16294727 2018-06 51,695 876 5.997 3
      SAMN16294728 2018-06 46,650 1,380 6.685 4
      SAMN16294729 2018-06 41,928 1,258 6.557 4
      SAMN16294730 2018-06 48,495 812 5.643 1
      SAMN16294731 2018-06 47,499 730 5.582 1
      SAMN16294732 2018-06 48,074 783 5.561 1
      SAMN16294733 2018-06 44,928 944 6.023 5
      SAMN16294734 2018-06 53,294 895 5.767 2
      SAMN16294735 2018-06 58,751 1,083 6.253 2
      SAMN16294736 2018-06 46,070 1,017 6.198 2
      SAMN16294737 2018-06 44,715 1,024 6.249 2
      SAMN16294738 2018-06 47,249 974 6.129 2
      SAMN16294739 2018-06 55,304 863 5.44 5
      SAMN16294740 2018-06 57,439 602 4.753 5

      click a column head to sort