## The number of loci caught by each filter.
## ipyrad API location: [assembly].stats_dfs.s7_filters

                           total_filters applied_order retained_loci
total_prefiltered_loci                 0             0            90
filtered_by_rm_duplicates              2             2            88
filtered_by_max_indels                 1             1            87
filtered_by_max_SNPs                   0             0            87
filtered_by_max_shared_het             2             2            85
filtered_by_min_sample                47            47            38
total_filtered_loci                   52            52            38


## The number of loci recovered for each Sample.
## ipyrad API location: [assembly].stats_dfs.s7_samples

                 sample_coverage
Cos_macrocarpa                 7
Ham_patens                    33
Hil_bonoi                     34
Hil_macbridei                 29
Hil_parasitica1               20
Hil_parasitica2               37
Hil_parasitica6                0
Hil_parasitica7               13
Hil_pumila1                    7
Hil_pumila2                    3
Hil_pumila3                    6
Hil_wurdackii1                 1
Hil_wurdackii2                21


## The number of loci for which N taxa have data.
## ipyrad API location: [assembly].stats_dfs.s7_loci

    locus_coverage  sum_coverage
1                0             0
2                0             0
3                0             0
4               15            15
5                7            22
6                9            31
7                2            33
8                1            34
9                2            36
10               1            37
11               0            37
12               1            38
13               0            38


The distribution of SNPs (var and pis) per locus.
## var = Number of loci with n variable sites (pis + autapomorphies)
## pis = Number of loci with n parsimony informative site (minor allele in >1 sample)
## ipyrad API location: [assembly].stats_dfs.s7_snps
## The "reference" sample is included if present unless 'exclude_reference=True'

   var  sum_var  pis  sum_pis
0   20        0   28        0
1   10       10    8        8
2    6       22    2       12
3    1       25    0       12
4    1       29    0       12


## Final Sample stats summary
                 state  reads_raw  reads_passed_filter  clusters_total  clusters_hidepth  hetero_est  error_est  reads_consens  loci_in_assembly
Cos_macrocarpa       7       1009                  980             601                 7    0.000033   0.000420              7                 7
Ham_patens           7      23353                22997            5704               271    0.037946   0.012334            134                33
Hil_bonoi            7      17629                17295            3488               162    0.016087   0.000913            135                34
Hil_macbridei        7       3618                 3581            1593                53    0.017196   0.001714             46                29
Hil_parasitica1      7       2243                 2219            1279                28    0.006976   0.001065             26                20
Hil_parasitica2      7      10270                10194            3165               114    0.024162   0.002784             85                37
Hil_parasitica6      7        785                  773             600                 1    0.000591   0.000093              1                 0
Hil_parasitica7      7       2238                 2169             709                24    0.019567   0.002284             18                13
Hil_pumila1          7       3563                 3475            2550                10    0.000090   0.000167             10                 7
Hil_pumila2          7       1201                 1180             869                 3    0.001307   0.000083              3                 3
Hil_pumila3          7       1390                 1339             906                 8    0.006018   0.000011              7                 6
Hil_wurdackii1       7         71                   70              45                 1    0.001307   0.000083              1                 1
Hil_wurdackii2       7       3746                 3670             974                66    0.023481   0.005645             41                21


## Alignment matrix statistics:
snps matrix size: (13, 29), 59.15% missing sites.
sequence matrix size: (13, 6003), 61.13% missing sites.