analysis_my_first_mothulity_project

cutoff at 0.03

Alpha Biodiversity

Biodiversity within a sample

Rarefaction

Rarefaction curves for the observed OTUs at a genetic distance of 0.03.

Citations:

MOTHUR command

Wikipedia article

OTU classification

Taxonomical representation of the observed OTUs.

Summary

label group method nseqs coverage sobs ace ace_lci ace_hci chao chao_lci chao_hci jackknife jackknife_lci jackknife_hci simpson simpson_lci simpson_hci invsimpson invsimpson_lci invsimpson_hci shannon shannon_lci shannon_hci npshannon
0.03 KA1k ave 646.0 0.972136 74.000000 88.047682 79.781457 108.132812 86.750000 78.138812 113.277575 92.000000 80.240000 103.760000 0.043987 0.038942 0.049032 22.734068 20.394978 25.679203 3.543859 3.454850 3.632867 3.630636
0.03 QA1k ave 646.0 0.964977 90.954000 108.104515 98.751818 128.783473 102.674778 95.227693 123.326784 114.801577 100.789405 128.813748 0.132483 0.108487 0.156480 7.573294 6.410267 9.252090 3.237452 3.097199 3.377705 3.384386
0.03 KA1k std 0.0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.03 QA1k std 0.0 0.005506 2.441287 6.356413 4.371354 9.908348 6.393211 3.888205 12.321173 18.707511 6.963912 31.135947 0.007601 0.006580 0.008626 0.440263 0.358034 0.568682 0.046200 0.047747 0.044718 0.045999

Citations:

MOTHUR command

Beta Biodiversity

Biodiversity among the samples

Dendrograms and Heatmaps

Dendrogram Jaccard

Dendrogram of the similarity between the communities based on Jaccard measurement. Relative scale.

Heatmap Jaccard

Community distance heatmap according to Jaccard measurement.

Dendrogram Yue and Clayton

Dendrogram of the similarity between the communities based on Yue and Clayton measurement. Relative scale.

Heatmap Yue and Clayton

Community distance heatmap according to Yue and Claytons measurement.

Citations:

MOTHUR command

NMDS

Non-metric multidimensional scaling (NMDS) analysis upon Jaccard measure of dissimilarity between all the samples. Proximity of the points on the plot reflects similarities of bacterial communities structure.

Non-metric multidimensional scaling (NMDS) analysis upon Yue and Clayton measure of dissimilarity between all the samples. Proximity of the points on the plot reflects similarities of bacterial communities structure.

Citations:

MOTHUR command

Wikipedia article