## 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 0 160
filtered_by_rm_duplicates 3 3 157
filtered_by_max_indels 5 5 152
filtered_by_max_SNPs 0 0 152
filtered_by_max_shared_het 8 8 144
filtered_by_min_sample 89 89 55
total_filtered_loci 105 105 55
## The number of loci recovered for each Sample.
## ipyrad API location: [assembly].stats_dfs.s7_samples
sample_coverage
KLU334 16
KLU95 18
KLU96 15
KLU98 19
ODE1 14
ODE14 7
ODE30 25
ODE36 21
ODE40 18
ODE56 23
SADAu12 11
SADAu7 11
SCA1 12
SCA101 10
SCA2 6
SCA85 1
SCA87 1
SCA94 21
TAS20 21
TAS21 18
VEN16 16
VEN5 2
VEN89 13
VEN96 14
## 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 24 24
5 5 29
6 5 34
7 7 41
8 6 47
9 3 50
10 4 54
11 0 54
12 0 54
13 0 54
14 0 54
15 0 54
16 0 54
17 0 54
18 1 55
19 0 55
20 0 55
21 0 55
22 0 55
23 0 55
24 0 55
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 8 0 21 0
1 13 13 9 9
2 3 19 8 25
3 6 37 1 28
4 1 41 4 44
5 0 41 5 69
6 3 59 0 69
7 6 101 2 83
8 3 125 0 83
9 3 152 1 92
10 0 152 1 102
11 0 152 0 102
12 0 152 1 114
13 2 178 0 114
14 1 192 1 128
15 0 192 0 128
16 0 192 0 128
17 2 226 0 128
18 0 226 1 146
19 0 226 0 146
20 0 226 0 146
21 0 226 0 146
22 0 226 0 146
23 1 249 0 146
24 0 249 0 146
25 1 274 0 146
26 0 274 0 146
27 0 274 0 146
28 0 274 0 146
29 0 274 0 146
30 0 274 0 146
31 1 305 0 146
32 0 305 0 146
33 0 305 0 146
34 0 305 0 146
35 0 305 0 146
36 0 305 0 146
37 0 305 0 146
38 1 343 0 146
## Final Sample stats summary
state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly
KLU334 7 8952 8872 4977 56 0.018069 0.006335 40 16
KLU95 7 12242 12102 5866 86 0.020807 0.005376 51 18
KLU96 7 12780 12639 6227 77 0.019695 0.006631 48 15
KLU98 7 12983 12848 7227 73 0.021419 0.006686 48 19
ODE1 7 9156 9058 4975 63 0.025020 0.007096 39 14
ODE14 7 5713 5647 2977 33 0.021280 0.006537 22 7
ODE30 7 14948 14784 7173 96 0.019896 0.006287 67 25
ODE36 7 16186 16011 7102 99 0.027102 0.005367 54 21
ODE40 7 16858 16671 7665 91 0.021136 0.006978 59 18
ODE56 7 17642 17440 8042 119 0.023680 0.005730 82 23
SADAu12 7 5415 5359 2648 31 0.022108 0.001610 23 11
SADAu7 7 4386 4326 2425 39 0.019500 0.008840 25 11
SCA1 7 9930 9862 4974 50 0.016940 0.009604 34 12
SCA101 7 6264 6183 3227 28 0.019527 0.007534 18 10
SCA2 7 8873 8805 4659 36 0.022877 0.005725 18 6
SCA85 7 65 63 40 2 0.042566 0.014730 2 1
SCA87 7 58 58 25 2 0.038093 0.016114 1 1
SCA94 7 10345 10219 5155 73 0.023654 0.004657 49 21
TAS20 7 19786 19613 9181 130 0.022997 0.005326 88 21
TAS21 7 12203 12056 6445 72 0.020247 0.006425 51 18
VEN16 7 14452 14312 6721 91 0.021742 0.007726 57 16
VEN5 7 1561 1543 1012 9 0.014446 0.006239 5 2
VEN89 7 6706 6623 3498 32 0.020292 0.010726 23 13
VEN96 7 11042 10940 5528 63 0.025229 0.009050 40 14
## Alignment matrix statistics:
snps matrix size: (24, 343), 79.45% missing sites.
sequence matrix size: (24, 11260), 76.67% missing sites.