Sampling depth issue

Per-sample sequence counts
Sequence count
Sample name
Kn4_Ent 150979
Sh3_PD 132266
Kn6_Endo3 126094
Kn2_PD 122577
Kn5_Endo1 117615
Sh1_SCU 107546
Kn10_Cl2 107019
Kn8_ICU 88132
Kn1_Endo2 86646
Kn9_IntCU 61892
Kn7_Ph 55527
Sh2_IntCCU 38724
Kn3_Cl1 136
here are mny sample sequence counts, the minimum one is 136 which is very smaller than the others and the maximum one!!! so which one can i choose to represent my sampling depth??

All samples except for Kn3_Cl1 have really good looking coverage (I can only imagine alpha-rarefaction would confirm this).

Definitely drop sample Kn3_Cl1. With coverage so much lower than all other samples, it is probably a failed sample and the reads could even represent contamination.

Use alpha-rarefaction to confirm that it is a reasonable sampling depth, but I’d recommend sampling at 38724 seqs (or thereabout).

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