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USEARCH v11

Example fastx_learn report


Training set:
19  Unique sequences (33 candidates, 14 filtered)
1.3e+008  Bases (134.6M)
2.2e+005  Substitution errors (222.3k)
2.5e+003  Deletion errors (2545.0)
1.7e+003  Insertion errors (1717.0)

0.001652  Sub error rate
0.000019  Del error rate
0.000013  Ins error rate

0.998348  Prob base correct
0.683735  Prob read correct (230 bases)

Sub counts: (row=base call, column=true base):
A           C           G           T
----------  ----------  ----------  ----------
A |  3.592e+007  1.448e+004  2.388e+004  5.246e+003
C |  1.394e+004  2.364e+007  7.098e+003  3.870e+004
G |  5.158e+004  2.680e+003  4.509e+007  3.625e+003
T |  6.336e+003  1.807e+004  3.670e+004  2.973e+007

Base call probs (row=base call, column=true base):
A           C           G           T
----------  ----------  ----------  ----------
A |   0.9987875   0.0004025   0.0006641   0.0001459
C |   0.0005880   0.9974800   0.0002995   0.0016326
G |   0.0011425   0.0000594   0.9987179   0.0000803
T |   0.0002127   0.0006064   0.0012318   0.9979491

Base call probs:
Call  True      Prob
A     A  0.998788
G     G  0.998718
T     T  0.997949
C     C  0.997480

C     T  0.001633
T     G  0.001232
G     A  0.001142
A     G  0.000664
T     C  0.000606
C     A  0.000588
A     C  0.000403
C     G  0.000299
T     A  0.000213
A     T  0.000146
G     T  0.000080
G     C  0.000059

230.0  Avg read length
0.001652  Substitution error rate
0.379871  Expected errors (by sub rate)
0.444000  Lambda (by Poisson least-squares best fit)
0.638093  Correct read frequency (obs)
0.683735  Correct read frequency (by sub rate)

Distribution of nr errors (Obs, Poisson least-squares, Poisson Lambda=E):
NrErrs    PctObs    PctFit      PctE
0     63.81     64.15     68.39
1     27.82     28.48     25.98
2      6.22      6.32      4.93
3      2.15      0.94      0.62

q   Q       Bases      Pct       Diffs      Pex     Pobs   Qobs
-  --  ----------  -------  ----------  -------  -------  -----
)   8          17    0.00%           0  0.15849  0.00000  41.00
,  11          34    0.00%           1  0.07943  0.02941  15.31
-  12          34    0.00%           0  0.06310  0.00000  41.00
/  14         481    0.00%           6  0.03981  0.01247  19.04
0  15         112    0.00%           2  0.03162  0.01786  17.48
1  16        1996    0.00%           6  0.02512  0.00301  25.22
2  17         508    0.00%           1  0.01995  0.00197  27.06
3  18         617    0.00%           8  0.01585  0.01297  18.87
4  19         985    0.00%           6  0.01259  0.00609  22.15
5  20         566    0.00%           3  0.01000  0.00530  22.76
6  21        1248    0.00%          10  0.00794  0.00801  20.96
7  22        4291    0.00%          29  0.00631  0.00676  21.70
8  23        5592    0.00%          56  0.00501  0.01001  19.99
9  24        2210    0.00%           6  0.00398  0.00271  25.66
:  25        9863    0.01%          25  0.00316  0.00253  25.96
;  26       17282    0.01%         162  0.00251  0.00937  20.28
<  27       25748    0.02%         214  0.00200  0.00831  20.80
=  28       22223    0.02%          64  0.00158  0.00288  25.41
>  29       44695    0.03%         356  0.00126  0.00797  20.99
?  30       74206    0.06%         414  0.00100  0.00558  22.53
@  31       42365    0.03%         401  0.00079  0.00947  20.24
A  32       51493    0.04%         374  0.00063  0.00726  21.39
B  33      124508    0.09%         713  0.00050  0.00573  22.42
C  34      164637    0.12%         990  0.00040  0.00601  22.21
D  35      207834    0.15%         850  0.00032  0.00409  23.88
E  36      213487    0.16%         541  0.00025  0.00253  25.96
F  37      265197    0.20%         746  0.00020  0.00281  25.51
G  38      304858    0.23%        1049  0.00016  0.00344  24.63
H  39      273547    0.20%         707  0.00013  0.00258  25.88
I  40      368565    0.27%         830  0.00010  0.00225  26.47
J  41   132379804   98.34%      213755  0.00008  0.00161  27.92