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