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Table 1 Mean (bold values) and standard deviation of population metrics for the final SNP panels using a de novo approach

From: Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species

   STA ALT COM MER
Manila clam Ho (± SD) 0.120 (0.014) 0.103 (0.005) 0.138 (0.017) 0.108 (0.010)
He (± SD) 0.163 (0.005) 0.135 (0.006) 0.170 (0.008) 0.140 (0.000)
Global FST 0.006 0.003 0.004 0.005
FIS (± SD) 0.237 (0.054) 0.251 (0.034) 0.195 (0.058) 0.228 (0.044)
AR (± SD) 1.698 (0.010) 1.660 (0.024) 1.713 (0.019) 1.668 (0.015)
STR (Groups) N N N N
Common cockle Ho (± SD) 0.145 (0.010) 0.125 (0.006) 0.150 (0.008) 0.133 (0.005)
He (±SD) 0.157 (0.005) 0.140 (0.000) 0.160 (0.000) 0.150 (0.000)
Global FST 0.033 0.029 0.032 0.030
FIS (± SD) 0.086 (0.028) 0.120 (0.026) 0.066 (0.036) 0.114 (0.029)
AR (± SD) 1.707 (0.026) 1.683 (0.024) 1.733 (0.024) 1.690 (0.022)
STR (Groups) Y (3) Y (3) Y (3) Y (3)
Brown trout Ho (± SD) 0.243 (0.023) 0.250 (0.035) 0.200 (0.026) 0.257 (0.029)
He (± SD) 0.190 (0.017) 0.187 (0.021) 0.170 (0.026) 0.193 (0.023)
Global FST 0.376 0.370 0.442 0.348
FIS (± SD) −0.269 (0.023) −0.336 (0.028) −0.179 (0.038) −0.333 (0.024)
AR (± SD) 1.523 (0.041) 1.520 (0.046) 1.470 (0.044) 1.533 (0.042)
STR (Groups) Y (2–3) Y (2–3) Y (2–3) Y (2–3)
Silver catfish Ho (± SD) 0.235 (0.049) 0.235 (0.049) 0.230 (0.057) 0.235 (0.049)
He (± SD) 0.230 (0.056) 0.230 (0.057) 0.230 (0.057) 0.235 (0.049)
Global FST 0.452 0.453 0.465 0.451
FIS (± SD) −0.004 (0.032) −0.012 (0.036) −0.002 (0.024) − 0.014 (0.038)
AR (± SD) 1.690 (0.180) 1.680 (0.170) 1.685 (0.177) 1.690 (0.170)
STR (Groups) Y (2) Y (2) Y (2) Y (2)
Small-spotted catshark Ho (± SD) 0.545 (0.021) 0.520 (0.000) 0.460 (0.028) 0.535 (0.007)
He (± SD) 0.355 (0.007) 0.340 (0.000) 0.325 (0.021) 0.340 (0.000)
Global FST 0.002 0.002 0.004 0.002
FIS (± SD) −0.528 (0.035) −0.541 (0.018) −0.406 (0.024) −0.544 (0.020)
AR (± SD) 1.925 (0.021) 1.905 (0.007) 1.915 (0.021) 1.915 (0.007)
STR (Groups) N N N N
  1. Mean observed heterozygosity across loci and populations (Ho), mean expected heterozygosity across loci and populations (He), global fixation index (global FST), mean inbreeding coefficient across populations (FIS), mean allelic richness across loci and populations (AR), number of population structure units detected using STRUCTURE (STR groups) are shown. Y represents structure and N represents no structure. The complete information can be found in Supplementary Information (Tables S1-S5)