training-diff-ksizes

estimated_probabilities.k11.txt

kmer size= 11
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 205503171, 'C': 192321024, 'T': 202910059, 'G': 194236790}
state counts= {'Ig_u': 8251, 'Ig_t': 227463, 'Ir_t': 1919898, 'Ir_u': 92814, 'M_u': 12518640, 'M_t': 780203978}
trans counts= {'Ir_t-Ir_t': 1085201, 'Ir_t-Ir_u': 4, 'M_u-Ir_t': 468, 'Ir_t-M_u': 3, 'M_t-Ig_t': 178959, 'Ig_t-M_u': 1, 'Ig_t-Ig_t': 48504, 'M_u-M_u': 63, 'M_u-M_t': 12518088, 'Ig_u-M_t': 8251, 'M_t-M_t': 766669253, 'M_t-Ir_t': 834188, 'Ig_t-M_t': 168373, 'Ir_t-M_t': 747240, 'M_t-Ir_u': 1, 'Ir_u-M_t': 92773, 'Ir_u-Ir_t': 41, 'M_t-M_u': 1045}
Ig_t-Ig_t	0.2132391
Ig_t-M_t	0.7402215
Ig_t-M_u	0.0000044
Ig_u-M_t	1.0000000
Ir_t-Ir_t	0.5652389
Ir_t-Ir_u	0.0000021
Ir_t-M_t	0.3892082
Ir_t-M_u	0.0000016
Ir_u-Ir_t	0.0004417
Ir_u-M_t	0.9995583
M_t-Ig_t	0.0002294
M_t-Ir_t	0.0010692
M_t-Ir_u	0.0000000
M_t-M_t	0.9826523
M_t-M_u	0.0000013
M_u-Ir_t	0.0000374
M_u-M_t	0.9999559
M_u-M_u	0.0000050

estimated_probabilities.k12.txt

kmer size= 12
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 202313923, 'C': 189196843, 'T': 199563310, 'G': 191278380}
state counts= {'Ig_u': 8312, 'Ig_t': 216441, 'Ir_t': 1827608, 'Ir_u': 84189, 'M_u': 13229059, 'M_t': 766986847}
trans counts= {'Ig_t-M_t': 160190, 'M_u-Ig_u': 38, 'M_u-Ig_t': 507, 'Ir_t-M_t': 718450, 'Ir_t-M_u': 1257, 'Ig_t-M_u': 238, 'Ir_u-M_t': 82330, 'Ir_u-M_u': 241, 'Ir_t-Ir_t': 1030305, 'Ir_t-Ir_u': 2765, 'Ig_t-Ig_t': 46112, 'Ig_t-Ig_u': 68, 'Ig_u-M_u': 38, 'Ig_u-M_t': 8162, 'Ir_u-Ir_u': 309, 'Ir_u-Ir_t': 1305, 'M_u-M_u': 127126, 'Ig_u-Ig_t': 97, 'M_t-Ir_u': 1527, 'M_t-Ir_t': 794574, 'Ig_u-Ig_u': 11, 'M_u-Ir_t': 1424, 'M_u-Ir_u': 244, 'M_u-M_t': 13086075, 'M_t-Ig_t': 169725, 'M_t-Ig_u': 320, 'M_t-M_t': 752931640, 'M_t-M_u': 568790}
Ig_t-Ig_t	0.2130465
Ig_t-Ig_u	0.0003142
Ig_t-M_t	0.7401093
Ig_t-M_u	0.0010996
Ig_u-Ig_t	0.0116699
Ig_u-Ig_u	0.0013234
Ig_u-M_t	0.9819538
Ig_u-M_u	0.0045717
Ir_t-Ir_t	0.5637451
Ir_t-Ir_u	0.0015129
Ir_t-M_t	0.3931095
Ir_t-M_u	0.0006878
Ir_u-Ir_t	0.0155008
Ir_u-Ir_u	0.0036703
Ir_u-M_t	0.9779187
Ir_u-M_u	0.0028626
M_t-Ig_t	0.0002213
M_t-Ig_u	0.0000004
M_t-Ir_t	0.0010360
M_t-Ir_u	0.0000020
M_t-M_t	0.9816748
M_t-M_u	0.0007416
M_u-Ig_t	0.0000383
M_u-Ig_u	0.0000029
M_u-Ir_t	0.0001076
M_u-Ir_u	0.0000184
M_u-M_t	0.9891917
M_u-M_u	0.0096096

estimated_probabilities.k13.txt

kmer size= 13
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 199185798, 'C': 186012405, 'T': 196233401, 'G': 188302264}
state counts= {'Ig_u': 15562, 'Ig_t': 198701, 'Ir_t': 1654505, 'Ir_u': 169264, 'M_u': 26727498, 'M_t': 740968338}
trans counts= {'Ig_t-M_t': 144823, 'M_u-Ig_u': 2641, 'M_u-Ig_t': 8444, 'Ig_t-M_u': 2957, 'Ir_t-M_u': 17967, 'Ir_t-M_t': 622226, 'Ir_u-M_t': 115454, 'Ir_u-M_u': 12205, 'Ir_t-Ir_t': 909602, 'Ir_t-Ir_u': 42299, 'Ig_t-Ig_t': 41344, 'Ig_t-Ig_u': 960, 'Ig_u-M_u': 1990, 'Ig_u-M_t': 11471, 'Ir_u-Ir_u': 21086, 'Ir_u-Ir_t': 20406, 'M_u-M_u': 6075252, 'M_u-M_t': 20336827, 'M_t-Ir_u': 26264, 'M_t-Ir_t': 709816, 'Ig_u-Ig_u': 604, 'M_u-Ir_t': 14681, 'M_u-Ir_u': 13464, 'Ig_u-Ig_t': 1440, 'M_t-Ig_t': 147473, 'M_t-Ig_u': 4135, 'M_t-M_t': 719737537, 'M_t-M_u': 8071912}
Ig_t-Ig_t	0.2080714
Ig_t-Ig_u	0.0048314
Ig_t-M_t	0.7288489
Ig_t-M_u	0.0148817
Ig_u-Ig_t	0.0925331
Ig_u-Ig_u	0.0388125
Ig_u-M_t	0.7371161
Ig_u-M_u	0.1278756
Ir_t-Ir_t	0.5497729
Ir_t-Ir_u	0.0255660
Ir_t-M_t	0.3760799
Ir_t-M_u	0.0108594
Ir_u-Ir_t	0.1205572
Ir_u-Ir_u	0.1245746
Ir_u-M_t	0.6820942
Ir_u-M_u	0.0721063
M_t-Ig_t	0.0001990
M_t-Ig_u	0.0000056
M_t-Ir_t	0.0009580
M_t-Ir_u	0.0000354
M_t-M_t	0.9713472
M_t-M_u	0.0108937
M_u-Ig_t	0.0003159
M_u-Ig_u	0.0000988
M_u-Ir_t	0.0005493
M_u-Ir_u	0.0005038
M_u-M_t	0.7608953
M_u-M_u	0.2273034

estimated_probabilities.k14.txt

kmer size= 14
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 196008982, 'C': 182882986, 'T': 192951983, 'G': 185271329}
state counts= {'Ig_u': 35938, 'Ig_t': 169235, 'Ir_t': 1312457, 'Ir_u': 437086, 'M_u': 63734755, 'M_t': 691425809}
trans counts= {'Ig_t-M_t': 119542, 'M_u-Ig_u': 15230, 'M_u-Ig_t': 23175, 'Ig_t-M_u': 6308, 'Ir_t-M_u': 41197, 'Ir_t-M_t': 437925, 'Ir_u-M_t': 189727, 'Ir_u-M_u': 69273, 'Ir_t-Ir_t': 687526, 'Ir_t-Ir_u': 95461, 'Ig_t-Ig_t': 33549, 'Ig_t-Ig_u': 1991, 'Ig_u-M_u': 11264, 'Ig_u-M_t': 17459, 'Ir_u-Ir_u': 134381, 'Ir_u-Ir_t': 43285, 'M_u-M_u': 33881904, 'M_u-M_t': 28685803, 'M_t-Ir_u': 66509, 'M_t-Ir_t': 551804, 'Ig_u-Ig_u': 3559, 'M_u-Ir_t': 29842, 'M_u-Ir_u': 86286, 'Ig_u-Ig_t': 3476, 'M_t-Ig_t': 109035, 'M_t-Ig_u': 8352, 'M_t-M_t': 661975353, 'M_t-M_u': 17167476}
Ig_t-Ig_t	0.1982391
Ig_t-Ig_u	0.0117647
Ig_t-M_t	0.7063669
Ig_t-M_u	0.0372736
Ig_u-Ig_t	0.0967221
Ig_u-Ig_u	0.0990317
Ig_u-M_t	0.4858089
Ig_u-M_u	0.3134287
Ir_t-Ir_t	0.5238465
Ir_t-Ir_u	0.0727346
Ir_t-M_t	0.3336681
Ir_t-M_u	0.0313892
Ir_u-Ir_t	0.0990309
Ir_u-Ir_u	0.3074475
Ir_u-M_t	0.4340725
Ir_u-M_u	0.1584883
M_t-Ig_t	0.0001577
M_t-Ig_u	0.0000121
M_t-Ir_t	0.0007981
M_t-Ir_u	0.0000962
M_t-M_t	0.9574062
M_t-M_u	0.0248291
M_u-Ig_t	0.0003636
M_u-Ig_u	0.0002390
M_u-Ir_t	0.0004682
M_u-Ir_u	0.0013538
M_u-M_t	0.4500810
M_u-M_u	0.5316080

estimated_probabilities.k15.txt

kmer size= 15
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 192803878, 'C': 179790372, 'T': 189612678, 'G': 182289764}
state counts= {'Ig_u': 56108, 'Ig_t': 140546, 'Ir_t': 955612, 'Ir_u': 732648, 'M_u': 101854446, 'M_t': 640757332}
trans counts= {'Ig_t-M_t': 98409, 'M_u-Ig_u': 32387, 'M_u-Ig_t': 32124, 'Ig_t-M_u': 6426, 'Ir_t-M_u': 45087, 'Ir_t-M_t': 279037, 'Ir_u-M_t': 234550, 'Ir_u-M_u': 153471, 'Ir_t-Ir_t': 482709, 'Ir_t-Ir_u': 108830, 'Ig_t-Ig_t': 27134, 'Ig_t-Ig_u': 1966, 'Ig_u-M_u': 24283, 'Ig_u-M_t': 19590, 'Ir_u-Ir_u': 306452, 'Ir_u-Ir_t': 37441, 'M_u-M_u': 72330408, 'M_u-M_t': 27433000, 'M_t-Ir_u': 68635, 'M_t-Ir_t': 408472, 'Ig_u-Ig_u': 7566, 'M_u-Ir_t': 26990, 'M_u-Ir_u': 204797, 'Ig_u-Ig_t': 4319, 'M_t-Ig_t': 76969, 'M_t-Ig_u': 7877, 'M_t-M_t': 612692746, 'M_t-M_u': 16726429}
Ig_t-Ig_t	0.1930613
Ig_t-Ig_u	0.0139883
Ig_t-M_t	0.7001907
Ig_t-M_u	0.0457217
Ig_u-Ig_t	0.0769765
Ig_u-Ig_u	0.1348471
Ig_u-M_t	0.3491481
Ig_u-M_u	0.4327903
Ir_t-Ir_t	0.5051307
Ir_t-Ir_u	0.1138851
Ir_t-M_t	0.2919982
Ir_t-M_u	0.0471813
Ir_u-Ir_t	0.0511037
Ir_u-Ir_u	0.4182800
Ir_u-M_t	0.3201401
Ir_u-M_u	0.2094744
M_t-Ig_t	0.0001201
M_t-Ig_u	0.0000123
M_t-Ir_t	0.0006375
M_t-Ir_u	0.0001071
M_t-M_t	0.9562009
M_t-M_u	0.0261042
M_u-Ig_t	0.0003154
M_u-Ig_u	0.0003180
M_u-Ir_t	0.0002650
M_u-Ir_u	0.0020107
M_u-M_t	0.2693353
M_u-M_u	0.7101350

estimated_probabilities.k16.txt

kmer size= 16
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 189654700, 'C': 176634939, 'T': 186302033, 'G': 179286432}
state counts= {'Ig_u': 69022, 'Ig_t': 119864, 'Ir_t': 682619, 'Ir_u': 955564, 'M_u': 127034144, 'M_t': 603016891}
trans counts= {'Ig_t-M_t': 84716, 'M_u-Ig_u': 45360, 'M_u-Ig_t': 34990, 'Ir_t-M_t': 185605, 'Ir_t-M_u': 34078, 'Ig_t-M_u': 4842, 'Ir_u-M_t': 244310, 'Ir_u-M_u': 225922, 'Ir_t-Ir_t': 333069, 'Ir_t-Ir_u': 99083, 'Ig_t-Ig_t': 23169, 'Ig_t-Ig_u': 1401, 'Ig_u-M_u': 34728, 'Ig_u-M_t': 18861, 'Ir_u-Ir_u': 462117, 'Ir_u-Ir_t': 22259, 'M_u-M_u': 101442087, 'M_u-M_t': 22839778, 'M_t-Ir_u': 55440, 'M_t-Ir_t': 309619, 'Ig_u-Ig_u': 10733, 'M_u-Ir_t': 17672, 'M_u-Ir_u': 304384, 'Ig_u-Ig_t': 4332, 'M_t-Ig_t': 57373, 'M_t-Ig_u': 6023, 'M_t-M_t': 579643621, 'M_t-M_u': 12713944}
Ig_t-Ig_t	0.1932941
Ig_t-Ig_u	0.0116882
Ig_t-M_t	0.7067677
Ig_t-M_u	0.0403958
Ig_u-Ig_t	0.0627626
Ig_u-Ig_u	0.1555011
Ig_u-M_t	0.2732607
Ig_u-M_u	0.5031439
Ir_t-Ir_t	0.4879281
Ir_t-Ir_u	0.1451512
Ir_t-M_t	0.2719013
Ir_t-M_u	0.0499224
Ir_u-Ir_t	0.0232941
Ir_u-Ir_u	0.4836065
Ir_u-M_t	0.2556710
Ir_u-M_u	0.2364279
M_t-Ig_t	0.0000951
M_t-Ig_u	0.0000100
M_t-Ir_t	0.0005134
M_t-Ir_u	0.0000919
M_t-M_t	0.9612394
M_t-M_u	0.0210839
M_u-Ig_t	0.0002754
M_u-Ig_u	0.0003571
M_u-Ir_t	0.0001391
M_u-Ir_u	0.0023961
M_u-M_t	0.1797924
M_u-M_u	0.7985419

estimated_probabilities.k17.txt

kmer size= 17
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 186461193, 'C': 173541994, 'T': 183028530, 'G': 176227799}
state counts= {'Ig_u': 76288, 'Ig_t': 105915, 'Ir_t': 489750, 'Ir_u': 1109254, 'M_u': 140902062, 'M_t': 576576247}
trans counts= {'Ig_t-M_t': 76224, 'M_u-Ig_u': 53762, 'M_u-Ig_t': 35322, 'Ig_t-M_u': 3131, 'Ir_t-M_u': 20020, 'Ir_t-M_t': 138832, 'Ir_u-M_t': 240378, 'Ir_u-M_u': 272751, 'Ir_t-Ir_t': 231618, 'Ir_t-Ir_u': 75922, 'Ig_t-Ig_t': 20866, 'Ig_t-Ig_u': 830, 'Ig_u-M_u': 41276, 'Ig_u-M_t': 17721, 'Ir_u-Ir_u': 582353, 'Ir_u-Ir_t': 12662, 'M_u-M_u': 118540418, 'M_u-M_t': 19190506, 'M_t-Ir_u': 49630, 'M_t-Ir_t': 234654, 'Ig_u-Ig_u': 12631, 'M_u-Ir_t': 10816, 'M_u-Ir_u': 374248, 'Ig_u-Ig_t': 4176, 'M_t-Ig_t': 45551, 'M_t-Ig_u': 4139, 'M_t-M_t': 556912586, 'M_t-M_u': 9437905}
Ig_t-Ig_t	0.1970070
Ig_t-Ig_u	0.0078365
Ig_t-M_t	0.7196714
Ig_t-M_u	0.0295614
Ig_u-Ig_t	0.0547399
Ig_u-Ig_u	0.1655699
Ig_u-M_t	0.2322908
Ig_u-M_u	0.5410549
Ir_t-Ir_t	0.4729311
Ir_t-Ir_u	0.1550219
Ir_t-M_t	0.2834752
Ir_t-M_u	0.0408780
Ir_u-Ir_t	0.0114149
Ir_u-Ir_u	0.5249952
Ir_u-M_t	0.2167024
Ir_u-M_u	0.2458869
M_t-Ig_t	0.0000790
M_t-Ig_u	0.0000072
M_t-Ir_t	0.0004070
M_t-Ir_u	0.0000861
M_t-M_t	0.9658958
M_t-M_u	0.0163689
M_u-Ig_t	0.0002507
M_u-Ig_u	0.0003816
M_u-Ir_t	0.0000768
M_u-Ir_u	0.0026561
M_u-M_t	0.1361975
M_u-M_u	0.8412965

estimated_probabilities.k18.txt

kmer size= 18
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 183233044, 'C': 170466102, 'T': 179707322, 'G': 173234460}
state counts= {'Ig_u': 79942, 'Ig_t': 96334, 'Ir_t': 359599, 'Ir_u': 1208940, 'M_u': 148652052, 'M_t': 556244061}
trans counts= {'Ig_t-M_t': 69961, 'M_u-Ig_u': 58755, 'M_u-Ig_t': 35161, 'Ig_t-M_u': 2471, 'Ir_t-M_u': 12647, 'Ir_t-M_t': 112054, 'Ir_u-M_t': 233945, 'Ir_u-M_u': 298396, 'Ir_t-Ir_t': 165523, 'Ir_t-Ir_u': 50974, 'Ig_t-Ig_t': 19310, 'Ig_t-Ig_u': 521, 'Ig_u-M_u': 44878, 'Ig_u-M_t': 16856, 'Ir_u-Ir_u': 667197, 'Ir_u-Ir_t': 8214, 'M_u-M_u': 127972346, 'M_u-M_t': 17217247, 'M_t-Ir_u': 38960, 'M_t-Ir_t': 178228, 'Ig_u-Ig_u': 13589, 'M_u-Ir_t': 7634, 'M_u-Ir_u': 430705, 'Ig_u-Ig_t': 4115, 'M_t-Ig_t': 37748, 'M_t-Ig_u': 2730, 'M_t-M_t': 538593998, 'M_t-M_u': 7728177}
Ig_t-Ig_t	0.2004484
Ig_t-Ig_u	0.0054083
Ig_t-M_t	0.7262337
Ig_t-M_u	0.0256503
Ig_u-Ig_t	0.0514748
Ig_u-Ig_u	0.1699857
Ig_u-M_t	0.2108529
Ig_u-M_u	0.5613820
Ir_t-Ir_t	0.4602988
Ir_t-Ir_u	0.1417523
Ir_t-M_t	0.3116082
Ir_t-M_u	0.0351697
Ir_u-Ir_t	0.0067944
Ir_u-Ir_u	0.5518859
Ir_u-M_t	0.1935125
Ir_u-M_u	0.2468245
M_t-Ig_t	0.0000679
M_t-Ig_u	0.0000049
M_t-Ir_t	0.0003204
M_t-Ir_u	0.0000700
M_t-M_t	0.9682692
M_t-M_u	0.0138935
M_u-Ig_t	0.0002365
M_u-Ig_u	0.0003953
M_u-Ir_t	0.0000514
M_u-Ir_u	0.0028974
M_u-M_t	0.1158225
M_u-M_u	0.8608852

estimated_probabilities.k19.txt

kmer size= 19
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 180060887, 'C': 167322781, 'T': 176424298, 'G': 170214374}
state counts= {'Ig_u': 82172, 'Ig_t': 88923, 'Ir_t': 272785, 'Ir_u': 1271981, 'M_u': 153590634, 'M_t': 538715845}
trans counts= {'Ig_t-M_t': 64750, 'M_u-Ig_u': 61829, 'M_u-Ig_t': 34861, 'Ig_t-M_u': 2089, 'Ir_t-M_u': 10442, 'Ir_t-M_t': 92425, 'Ir_u-M_t': 228702, 'Ir_u-M_u': 313730, 'Ir_t-Ir_t': 120599, 'Ir_t-Ir_u': 34337, 'Ig_t-Ig_t': 18017, 'Ig_t-Ig_u': 413, 'Ig_u-M_u': 47356, 'Ig_u-M_t': 16058, 'Ir_u-Ir_u': 721796, 'Ir_u-Ir_t': 6538, 'M_u-M_u': 133625975, 'M_u-M_t': 16284732, 'M_t-Ir_u': 26071, 'M_t-Ir_t': 139398, 'Ig_u-Ig_u': 14151, 'M_u-Ir_t': 6250, 'M_u-Ir_u': 472857, 'Ig_u-Ig_t': 4045, 'M_t-Ig_t': 32000, 'M_t-Ig_u': 2038, 'M_t-M_t': 522029178, 'M_t-M_u': 6993115}
Ig_t-Ig_t	0.2026135
Ig_t-Ig_u	0.0046445
Ig_t-M_t	0.7281581
Ig_t-M_u	0.0234922
Ig_u-Ig_t	0.0492260
Ig_u-Ig_u	0.1722119
Ig_u-M_t	0.1954194
Ig_u-M_u	0.5763034
Ir_t-Ir_t	0.4421028
Ir_t-Ir_u	0.1258757
Ir_t-M_t	0.3388199
Ir_t-M_u	0.0382792
Ir_u-Ir_t	0.0051400
Ir_u-Ir_u	0.5674582
Ir_u-M_t	0.1797999
Ir_u-M_u	0.2466468
M_t-Ig_t	0.0000594
M_t-Ig_u	0.0000038
M_t-Ir_t	0.0002588
M_t-Ir_u	0.0000484
M_t-M_t	0.9690251
M_t-M_u	0.0129811
M_u-Ig_t	0.0002270
M_u-Ig_u	0.0004026
M_u-Ir_t	0.0000407
M_u-Ir_u	0.0030787
M_u-M_t	0.1060269
M_u-M_u	0.8700138

estimated_probabilities.k20.txt

kmer size= 20
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 176844469, 'C': 164244874, 'T': 173181507, 'G': 167132902}
state counts= {'Ig_u': 83750, 'Ig_t': 82596, 'Ir_t': 210307, 'Ir_u': 1315533, 'M_u': 157316340, 'M_t': 522395226}
trans counts= {'Ig_t-M_t': 60516, 'M_u-Ig_u': 63873, 'M_u-Ig_t': 34608, 'Ig_t-M_u': 1733, 'Ir_t-M_u': 9102, 'Ir_t-M_t': 76359, 'Ir_u-M_t': 224654, 'Ir_u-M_u': 325895, 'Ir_t-Ir_t': 89163, 'Ir_t-Ir_u': 23403, 'Ig_t-Ig_t': 16922, 'Ig_t-Ig_u': 316, 'Ig_u-M_u': 49382, 'Ig_u-M_t': 15294, 'Ir_u-Ir_u': 757741, 'Ir_u-Ir_t': 5961, 'M_u-M_u': 137689311, 'M_u-M_t': 15742696, 'M_t-Ir_u': 19970, 'M_t-Ir_t': 109487, 'Ig_u-Ig_u': 14555, 'M_u-Ir_t': 5696, 'M_u-Ir_u': 500228, 'Ig_u-Ig_t': 4000, 'M_t-Ig_t': 27066, 'M_t-Ig_u': 1798, 'M_t-M_t': 506275707, 'M_t-M_u': 6639728}
Ig_t-Ig_t	0.2048767
Ig_t-Ig_u	0.0038259
Ig_t-M_t	0.7326747
Ig_t-M_u	0.0209816
Ig_u-Ig_t	0.0477612
Ig_u-Ig_u	0.1737910
Ig_u-M_t	0.1826149
Ig_u-M_u	0.5896358
Ir_t-Ir_t	0.4239659
Ir_t-Ir_u	0.1112802
Ir_t-M_t	0.3630835
Ir_t-M_u	0.0432796
Ir_u-Ir_t	0.0045312
Ir_u-Ir_u	0.5759954
Ir_u-M_t	0.1707703
Ir_u-M_u	0.2477285
M_t-Ig_t	0.0000518
M_t-Ig_u	0.0000034
M_t-Ir_t	0.0002096
M_t-Ir_u	0.0000382
M_t-M_t	0.9691431
M_t-M_u	0.0127102
M_u-Ig_t	0.0002200
M_u-Ig_u	0.0004060
M_u-Ir_t	0.0000362
M_u-Ir_u	0.0031798
M_u-M_t	0.1000703
M_u-M_u	0.8752385

estimated_probabilities.k21.txt

kmer size= 21
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 173595055, 'C': 161183014, 'T': 169885267, 'G': 164121828}
state counts= {'Ig_u': 84943, 'Ig_t': 77340, 'Ir_t': 163927, 'Ir_u': 1345897, 'M_u': 160392782, 'M_t': 506720275}
trans counts= {'Ir_t-M_u': 6999, 'M_u-Ig_u': 65666, 'M_u-Ig_t': 34246, 'Ig_t-M_u': 1312, 'Ig_t-M_t': 57015, 'Ir_t-M_t': 63752, 'Ir_u-M_t': 220835, 'Ir_u-M_u': 336278, 'Ir_t-Ir_t': 66870, 'Ir_t-Ir_u': 15999, 'Ig_t-Ig_t': 16030, 'Ig_t-Ig_u': 218, 'Ig_u-M_u': 50913, 'Ig_u-M_t': 14744, 'Ir_u-Ir_u': 781860, 'Ir_u-Ir_t': 5609, 'M_u-M_u': 140981290, 'M_u-M_t': 15364986, 'M_t-Ir_u': 15593, 'M_t-Ir_t': 86032, 'Ig_u-Ig_u': 14817, 'M_u-Ir_t': 5416, 'M_u-Ir_u': 520708, 'Ig_u-Ig_t': 3973, 'M_t-Ig_t': 23091, 'M_t-Ig_u': 1469, 'M_t-M_t': 490998943, 'M_t-M_u': 6411912}
Ig_t-Ig_t	0.2072666
Ig_t-Ig_u	0.0028187
Ig_t-M_t	0.7371994
Ig_t-M_u	0.0169641
Ig_u-Ig_t	0.0467725
Ig_u-Ig_u	0.1744346
Ig_u-M_t	0.1735752
Ig_u-M_u	0.5993784
Ir_t-Ir_t	0.4079255
Ir_t-Ir_u	0.0975983
Ir_t-M_t	0.3889048
Ir_t-M_u	0.0426958
Ir_u-Ir_t	0.0041675
Ir_u-Ir_u	0.5809211
Ir_u-M_t	0.1640802
Ir_u-M_u	0.2498542
M_t-Ig_t	0.0000456
M_t-Ig_u	0.0000029
M_t-Ir_t	0.0001698
M_t-Ir_u	0.0000308
M_t-M_t	0.9689743
M_t-M_u	0.0126538
M_u-Ig_t	0.0002135
M_u-Ig_u	0.0004094
M_u-Ir_t	0.0000338
M_u-Ir_u	0.0032465
M_u-M_t	0.0957960
M_u-M_u	0.8789753

estimated_probabilities.k22.txt

kmer size= 22
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 170402613, 'C': 158060929, 'T': 166618517, 'G': 161084517}
state counts= {'Ig_u': 85668, 'Ig_t': 73015, 'Ir_t': 129753, 'Ir_u': 1366380, 'M_u': 163023048, 'M_t': 491488712}
trans counts= {'Ir_t-M_u': 4680, 'M_u-Ig_u': 67096, 'M_u-Ig_t': 33909, 'Ig_t-M_u': 1005, 'Ig_t-M_t': 54243, 'Ir_t-M_t': 54630, 'Ir_u-M_t': 217538, 'Ir_u-M_u': 344200, 'Ir_t-Ir_t': 51752, 'Ir_t-Ir_u': 10291, 'Ig_t-Ig_t': 15286, 'Ig_t-Ig_u': 180, 'Ig_u-M_u': 51952, 'Ig_u-M_t': 14308, 'Ir_u-Ir_u': 797870, 'Ir_u-Ir_t': 5548, 'M_u-M_u': 143749639, 'M_u-M_t': 15079781, 'M_t-Ir_u': 12127, 'M_t-Ir_t': 67255, 'Ig_u-Ig_u': 15001, 'M_u-Ir_t': 5198, 'M_u-Ir_u': 536424, 'Ig_u-Ig_t': 3937, 'M_t-Ig_t': 19883, 'M_t-Ig_u': 957, 'M_t-M_t': 476068212, 'M_t-M_u': 6265086}
Ig_t-Ig_t	0.2093542
Ig_t-Ig_u	0.0024652
Ig_t-M_t	0.7429021
Ig_t-M_u	0.0137643
Ig_u-Ig_t	0.0459565
Ig_u-Ig_u	0.1751062
Ig_u-M_t	0.1670169
Ig_u-M_u	0.6064341
Ir_t-Ir_t	0.3988501
Ir_t-Ir_u	0.0793122
Ir_t-M_t	0.4210307
Ir_t-M_u	0.0360685
Ir_u-Ir_t	0.0040604
Ir_u-Ir_u	0.5839298
Ir_u-M_t	0.1592075
Ir_u-M_u	0.2519065
M_t-Ig_t	0.0000405
M_t-Ig_u	0.0000019
M_t-Ir_t	0.0001368
M_t-Ir_u	0.0000247
M_t-M_t	0.9686249
M_t-M_u	0.0127472
M_u-Ig_t	0.0002080
M_u-Ig_u	0.0004116
M_u-Ir_t	0.0000319
M_u-Ir_u	0.0032905
M_u-M_t	0.0925009
M_u-M_u	0.8817749

estimated_probabilities.k23.txt

kmer size= 23
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 167170973, 'C': 154995473, 'T': 163404457, 'G': 157977085}
state counts= {'Ig_u': 86151, 'Ig_t': 69526, 'Ir_t': 106014, 'Ir_u': 1378462, 'M_u': 165327463, 'M_t': 476580372}
trans counts= {'Ig_t-M_t': 51933, 'M_u-Ig_u': 67970, 'M_u-Ig_t': 33579, 'Ig_t-M_u': 884, 'Ir_t-M_u': 3380, 'Ir_t-M_t': 47911, 'Ir_u-M_t': 214295, 'Ir_u-M_u': 349625, 'Ir_t-Ir_t': 42722, 'Ir_t-Ir_u': 5584, 'Ig_t-Ig_t': 14669, 'Ig_t-Ig_u': 183, 'Ig_u-M_u': 52698, 'Ig_u-M_t': 13956, 'Ir_u-Ir_u': 807962, 'Ir_u-Ir_t': 5424, 'Ig_u-Ig_u': 15133, 'M_u-M_t': 14815838, 'M_t-Ir_u': 8835, 'M_t-Ir_t': 52870, 'M_u-M_u': 146167888, 'M_u-Ir_t': 4998, 'M_u-Ir_u': 548446, 'Ig_u-Ig_t': 3901, 'M_t-Ig_t': 17377, 'M_t-Ig_u': 666, 'M_t-M_t': 461436439, 'M_t-M_u': 6144234}
Ig_t-Ig_t	0.2109858
Ig_t-Ig_u	0.0026321
Ig_t-M_t	0.7469580
Ig_t-M_u	0.0127147
Ig_u-Ig_t	0.0452810
Ig_u-Ig_u	0.1756567
Ig_u-M_t	0.1619946
Ig_u-M_u	0.6116934
Ir_t-Ir_t	0.4029845
Ir_t-Ir_u	0.0526723
Ir_t-M_t	0.4519309
Ir_t-M_u	0.0318826
Ir_u-Ir_t	0.0039348
Ir_u-Ir_u	0.5861330
Ir_u-M_t	0.1554595
Ir_u-M_u	0.2536341
M_t-Ig_t	0.0000365
M_t-Ig_u	0.0000014
M_t-Ir_t	0.0001109
M_t-Ir_u	0.0000185
M_t-M_t	0.9682238
M_t-M_u	0.0128923
M_u-Ig_t	0.0002031
M_u-Ig_u	0.0004111
M_u-Ir_t	0.0000302
M_u-Ir_u	0.0033173
M_u-M_t	0.0896151
M_u-M_u	0.8841114

estimated_probabilities.k24.txt

kmer size= 24
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 163904240, 'C': 151949777, 'T': 160126108, 'G': 154949275}
state counts= {'Ig_u': 86441, 'Ig_t': 66624, 'Ir_t': 90567, 'Ir_u': 1384414, 'M_u': 167344351, 'M_t': 461957003}
trans counts= {'Ir_t-M_u': 2484, 'M_u-Ig_u': 68601, 'M_u-Ig_t': 33215, 'Ig_t-M_u': 699, 'Ig_t-M_t': 50108, 'Ir_t-M_t': 42888, 'Ir_u-M_t': 211087, 'Ir_u-M_u': 353906, 'Ir_t-Ir_t': 37327, 'Ir_t-Ir_u': 3114, 'Ig_t-Ig_t': 14146, 'Ig_t-Ig_u': 131, 'Ig_u-M_u': 53312, 'Ig_u-M_t': 13572, 'Ir_u-Ir_u': 813042, 'Ir_u-Ir_t': 5390, 'Ig_u-Ig_u': 15251, 'M_u-M_t': 14586173, 'M_t-Ir_u': 5657, 'M_t-Ir_t': 43032, 'M_u-M_u': 148286329, 'M_u-Ir_t': 4818, 'M_u-Ir_u': 556888, 'Ig_u-Ig_t': 3882, 'M_t-Ig_t': 15381, 'M_t-Ig_u': 551, 'M_t-M_t': 447053175, 'M_t-M_u': 6036653}
Ig_t-Ig_t	0.2123259
Ig_t-Ig_u	0.0019663
Ig_t-M_t	0.7521013
Ig_t-M_u	0.0104917
Ig_u-Ig_t	0.0449092
Ig_u-Ig_u	0.1764325
Ig_u-M_t	0.1570088
Ig_u-M_u	0.6167444
Ir_t-Ir_t	0.4121479
Ir_t-Ir_u	0.0343834
Ir_t-M_t	0.4735500
Ir_t-M_u	0.0274272
Ir_u-Ir_t	0.0038933
Ir_u-Ir_u	0.5872824
Ir_u-M_t	0.1524739
Ir_u-M_u	0.2556360
M_t-Ig_t	0.0000333
M_t-Ig_u	0.0000012
M_t-Ir_t	0.0000932
M_t-Ir_u	0.0000122
M_t-M_t	0.9677376
M_t-M_u	0.0130676
M_u-Ig_t	0.0001985
M_u-Ig_u	0.0004099
M_u-Ir_t	0.0000288
M_u-Ir_u	0.0033278
M_u-M_t	0.0871626
M_u-M_u	0.8861149

estimated_probabilities.k25.txt

kmer size= 25
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 160702949, 'C': 148835916, 'T': 156870576, 'G': 151901371}
state counts= {'Ig_u': 86433, 'Ig_t': 64287, 'Ir_t': 80354, 'Ir_u': 1387443, 'M_u': 169093858, 'M_t': 447598437}
trans counts= {'Ig_t-M_t': 48615, 'M_u-Ig_u': 69088, 'M_u-Ig_t': 32888, 'Ig_t-M_u': 609, 'Ir_t-M_u': 1638, 'Ir_t-M_t': 39334, 'Ir_u-M_t': 208456, 'Ir_u-M_u': 357143, 'Ir_t-Ir_t': 33914, 'Ir_t-Ir_u': 2028, 'Ig_t-Ig_t': 13711, 'Ig_t-Ig_u': 122, 'Ig_u-M_u': 53744, 'Ig_u-M_t': 13141, 'Ir_u-Ir_u': 815657, 'Ir_u-Ir_t': 5300, 'Ig_u-Ig_u': 15327, 'M_u-M_t': 14390195, 'M_t-Ir_u': 3491, 'M_t-Ir_t': 36409, 'M_u-M_u': 150113622, 'M_u-Ir_t': 4731, 'M_u-Ir_u': 561995, 'Ig_u-Ig_t': 3858, 'M_t-Ig_t': 13830, 'M_t-Ig_u': 370, 'M_t-M_t': 432898696, 'M_t-M_u': 5954312}
Ig_t-Ig_t	0.2132780
Ig_t-Ig_u	0.0018977
Ig_t-M_t	0.7562182
Ig_t-M_u	0.0094731
Ig_u-Ig_t	0.0446357
Ig_u-Ig_u	0.1773281
Ig_u-M_t	0.1520368
Ig_u-M_u	0.6217995
Ir_t-Ir_t	0.4220574
Ir_t-Ir_u	0.0252383
Ir_t-M_t	0.4895089
Ir_t-M_u	0.0203848
Ir_u-Ir_t	0.0038200
Ir_u-Ir_u	0.5878851
Ir_u-M_t	0.1502447
Ir_u-M_u	0.2574109
M_t-Ig_t	0.0000309
M_t-Ig_u	0.0000008
M_t-Ir_t	0.0000813
M_t-Ir_u	0.0000078
M_t-M_t	0.9671586
M_t-M_u	0.0133028
M_u-Ig_t	0.0001945
M_u-Ig_u	0.0004086
M_u-Ir_t	0.0000280
M_u-Ir_u	0.0033236
M_u-M_t	0.0851018
M_u-M_u	0.8877533

estimated_probabilities.k26.txt

kmer size= 26
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 157453235, 'C': 145771089, 'T': 153670787, 'G': 148797113}
state counts= {'Ig_u': 86540, 'Ig_t': 62386, 'Ir_t': 73580, 'Ir_u': 1388752, 'M_u': 170621991, 'M_t': 433458975}
trans counts= {'Ir_t-M_u': 1088, 'M_u-Ig_u': 69422, 'M_u-Ig_t': 32553, 'Ig_t-M_u': 524, 'Ig_t-M_t': 47477, 'Ir_t-M_t': 36969, 'Ir_u-M_t': 206008, 'Ir_u-M_u': 359616, 'Ir_t-Ir_t': 31844, 'Ir_t-Ir_u': 1342, 'Ig_t-Ig_t': 13351, 'Ig_t-Ig_u': 132, 'Ig_u-M_u': 54110, 'Ig_u-M_t': 12885, 'Ir_u-Ir_u': 817110, 'Ir_u-Ir_t': 5207, 'Ig_u-Ig_u': 15405, 'M_u-M_t': 14189853, 'M_t-Ir_u': 2290, 'M_t-Ir_t': 31869, 'M_u-M_u': 151727814, 'M_u-Ir_t': 4660, 'M_u-Ir_u': 564876, 'Ig_u-Ig_t': 3831, 'M_t-Ig_t': 12651, 'M_t-Ig_u': 256, 'M_t-M_t': 418965783, 'M_t-M_u': 5864710}
Ig_t-Ig_t	0.2140063
Ig_t-Ig_u	0.0021159
Ig_t-M_t	0.7610201
Ig_t-M_u	0.0083993
Ig_u-Ig_t	0.0442685
Ig_u-Ig_u	0.1780102
Ig_u-M_t	0.1488907
Ig_u-M_u	0.6252600
Ir_t-Ir_t	0.4327806
Ir_t-Ir_u	0.0182387
Ir_t-M_t	0.5024327
Ir_t-M_u	0.0147866
Ir_u-Ir_t	0.0037494
Ir_u-Ir_u	0.5883772
Ir_u-M_t	0.1483404
Ir_u-M_u	0.2589490
M_t-Ig_t	0.0000292
M_t-Ig_u	0.0000006
M_t-Ir_t	0.0000735
M_t-Ir_u	0.0000053
M_t-M_t	0.9665639
M_t-M_u	0.0135300
M_u-Ig_t	0.0001908
M_u-Ig_u	0.0004069
M_u-Ir_t	0.0000273
M_u-Ir_u	0.0033107
M_u-M_t	0.0831654
M_u-M_u	0.8892629

estimated_probabilities.k27.txt

kmer size= 27
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 154177851, 'C': 142736071, 'T': 150397751, 'G': 145761963}
state counts= {'Ig_u': 86608, 'Ig_t': 60888, 'Ir_t': 69200, 'Ir_u': 1389076, 'M_u': 171919989, 'M_t': 419547875}
trans counts= {'Ir_t-M_u': 829, 'M_u-Ig_u': 69675, 'M_u-Ig_t': 32229, 'Ig_t-M_u': 500, 'Ig_t-M_t': 46522, 'Ir_t-M_t': 35289, 'Ir_u-M_t': 203727, 'Ir_u-M_u': 361636, 'Ir_t-Ir_t': 30563, 'Ir_t-Ir_u': 934, 'Ig_t-Ig_t': 13068, 'Ig_t-Ig_u': 122, 'Ig_u-M_u': 54391, 'Ig_u-M_t': 12643, 'Ir_u-Ir_u': 817962, 'Ir_u-Ir_t': 5143, 'Ig_u-Ig_u': 15496, 'Ig_u-Ig_t': 3817, 'M_t-Ir_u': 1489, 'M_t-Ir_t': 28929, 'M_u-M_u': 153102894, 'M_u-Ir_t': 4565, 'M_u-Ir_u': 566465, 'M_u-M_t': 14008369, 'M_t-Ig_t': 11774, 'M_t-Ig_u': 209, 'M_t-M_t': 405241325, 'M_t-M_u': 5784483}
Ig_t-Ig_t	0.2146236
Ig_t-Ig_u	0.0020037
Ig_t-M_t	0.7640586
Ig_t-M_u	0.0082118
Ig_u-Ig_t	0.0440721
Ig_u-Ig_u	0.1789211
Ig_u-M_t	0.1459796
Ig_u-M_u	0.6280136
Ir_t-Ir_t	0.4416618
Ir_t-Ir_u	0.0134971
Ir_t-M_t	0.5099566
Ir_t-M_u	0.0119798
Ir_u-Ir_t	0.0037025
Ir_u-Ir_u	0.5888533
Ir_u-M_t	0.1466637
Ir_u-M_u	0.2603428
M_t-Ig_t	0.0000281
M_t-Ig_u	0.0000005
M_t-Ir_t	0.0000690
M_t-Ir_u	0.0000035
M_t-M_t	0.9659001
M_t-M_u	0.0137874
M_u-Ig_t	0.0001875
M_u-Ig_u	0.0004053
M_u-Ir_t	0.0000266
M_u-Ir_u	0.0032949
M_u-M_t	0.0814819
M_u-M_u	0.8905474

estimated_probabilities.k28.txt

kmer size= 28
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 150972513, 'C': 139625178, 'T': 147148452, 'G': 142708905}
state counts= {'Ig_u': 86637, 'Ig_t': 59671, 'Ir_t': 66295, 'Ir_u': 1389073, 'M_u': 173013979, 'M_t': 405839393}
trans counts= {'Ir_t-M_u': 619, 'M_u-Ig_u': 69922, 'M_u-Ig_t': 31888, 'Ig_t-M_u': 472, 'Ig_t-M_t': 45718, 'Ir_t-M_t': 34039, 'Ir_u-M_t': 201759, 'Ir_u-M_u': 363315, 'Ir_t-Ir_t': 29787, 'Ir_t-Ir_u': 786, 'Ig_t-Ig_t': 12828, 'Ig_t-Ig_u': 117, 'Ig_u-M_u': 54696, 'Ig_u-M_t': 12340, 'Ir_u-Ir_u': 818410, 'Ir_u-Ir_t': 5040, 'Ig_u-Ig_u': 15587, 'M_u-M_t': 13846437, 'M_t-Ir_u': 957, 'M_t-Ir_t': 26996, 'M_u-M_u': 154260926, 'M_u-Ir_t': 4472, 'M_u-Ir_u': 567409, 'Ig_u-Ig_t': 3801, 'M_t-Ig_t': 11154, 'M_t-Ig_u': 156, 'M_t-M_t': 391699100, 'M_t-M_u': 5717729}
Ig_t-Ig_t	0.2149788
Ig_t-Ig_u	0.0019608
Ig_t-M_t	0.7661678
Ig_t-M_u	0.0079100
Ig_u-Ig_t	0.0438727
Ig_u-Ig_u	0.1799116
Ig_u-M_t	0.1424334
Ig_u-M_u	0.6313238
Ir_t-Ir_t	0.4493099
Ir_t-Ir_u	0.0118561
Ir_t-M_t	0.5134475
Ir_t-M_u	0.0093371
Ir_u-Ir_t	0.0036283
Ir_u-Ir_u	0.5891771
Ir_u-M_t	0.1452472
Ir_u-M_u	0.2615521
M_t-Ig_t	0.0000275
M_t-Ig_u	0.0000004
M_t-Ir_t	0.0000665
M_t-Ir_u	0.0000024
M_t-M_t	0.9651579
M_t-M_u	0.0140886
M_u-Ig_t	0.0001843
M_u-Ig_u	0.0004041
M_u-Ir_t	0.0000258
M_u-Ir_u	0.0032796
M_u-M_t	0.0800307
M_u-M_u	0.8916096

estimated_probabilities.k29.txt

kmer size= 29
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 147724646, 'C': 136567813, 'T': 143945222, 'G': 139598779}
state counts= {'Ig_u': 86758, 'Ig_t': 58623, 'Ir_t': 64314, 'Ir_u': 1389082, 'M_u': 173928749, 'M_t': 392308934}
trans counts= {'Ir_t-M_u': 465, 'M_u-Ig_u': 70153, 'M_u-Ig_t': 31527, 'Ig_t-M_u': 429, 'Ig_t-M_t': 45029, 'Ir_t-M_t': 33161, 'Ir_u-M_t': 200073, 'Ir_u-M_u': 364902, 'Ir_t-Ir_t': 29230, 'Ir_t-Ir_u': 727, 'Ig_t-Ig_t': 12623, 'Ig_t-Ig_u': 105, 'Ig_u-M_u': 54979, 'Ig_u-M_t': 12116, 'Ir_u-Ir_u': 818685, 'Ir_u-Ir_t': 4989, 'Ig_u-Ig_u': 15693, 'M_u-M_t': 13666322, 'M_t-Ir_u': 773, 'M_t-Ir_t': 25665, 'M_u-M_u': 155227348, 'M_u-Ir_t': 4430, 'M_u-Ir_u': 567745, 'Ig_u-Ig_t': 3775, 'M_t-Ig_t': 10698, 'M_t-Ig_u': 130, 'M_t-M_t': 378352233, 'M_t-M_u': 5663867}
Ig_t-Ig_t	0.2153250
Ig_t-Ig_u	0.0017911
Ig_t-M_t	0.7681115
Ig_t-M_u	0.0073179
Ig_u-Ig_t	0.0435118
Ig_u-Ig_u	0.1808825
Ig_u-M_t	0.1396528
Ig_u-M_u	0.6337052
Ir_t-Ir_t	0.4544889
Ir_t-Ir_u	0.0113039
Ir_t-M_t	0.5156109
Ir_t-M_u	0.0072302
Ir_u-Ir_t	0.0035916
Ir_u-Ir_u	0.5893713
Ir_u-M_t	0.1440325
Ir_u-M_u	0.2626929
M_t-Ig_t	0.0000273
M_t-Ig_u	0.0000003
M_t-Ir_t	0.0000654
M_t-Ir_u	0.0000020
M_t-M_t	0.9644242
M_t-M_u	0.0144373
M_u-Ig_t	0.0001813
M_u-Ig_u	0.0004033
M_u-Ir_t	0.0000255
M_u-Ir_u	0.0032642
M_u-M_t	0.0785743
M_u-M_u	0.8924767

estimated_probabilities.k30.txt

kmer size= 30
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 144454720, 'C': 133529144, 'T': 140678610, 'G': 136555398}
state counts= {'Ig_u': 86973, 'Ig_t': 57725, 'Ir_t': 62885, 'Ir_u': 1389091, 'M_u': 174651791, 'M_t': 378969407}
trans counts= {'Ir_t-M_u': 373, 'M_u-Ig_u': 70341, 'M_u-Ig_t': 31210, 'Ig_t-M_u': 408, 'Ig_t-M_t': 44419, 'Ir_t-M_t': 32511, 'Ir_u-M_t': 198397, 'Ir_u-M_u': 366430, 'Ir_t-Ir_t': 28819, 'Ir_t-Ir_u': 643, 'Ig_t-Ig_t': 12427, 'Ig_t-Ig_u': 121, 'Ig_u-M_u': 55252, 'Ig_u-M_t': 12010, 'Ir_u-Ir_u': 818966, 'Ir_u-Ir_t': 4949, 'Ig_u-Ig_u': 15783, 'M_u-M_t': 13490036, 'M_t-Ir_u': 620, 'M_t-Ir_t': 24770, 'M_u-M_u': 156034825, 'M_u-Ir_t': 4347, 'M_u-Ir_u': 567966, 'Ig_u-Ig_t': 3742, 'M_t-Ig_t': 10346, 'M_t-Ig_u': 102, 'M_t-M_t': 365192034, 'M_t-M_u': 5577437}
Ig_t-Ig_t	0.2152793
Ig_t-Ig_u	0.0020961
Ig_t-M_t	0.7694933
Ig_t-M_u	0.0070680
Ig_u-Ig_t	0.0430248
Ig_u-Ig_u	0.1814701
Ig_u-M_t	0.1380888
Ig_u-M_u	0.6352776
Ir_t-Ir_t	0.4582810
Ir_t-Ir_u	0.0102250
Ir_t-M_t	0.5169913
Ir_t-M_u	0.0059315
Ir_u-Ir_t	0.0035628
Ir_u-Ir_u	0.5895697
Ir_u-M_t	0.1428251
Ir_u-M_u	0.2637912
M_t-Ig_t	0.0000273
M_t-Ig_u	0.0000003
M_t-Ir_t	0.0000654
M_t-Ir_u	0.0000016
M_t-M_t	0.9636452
M_t-M_u	0.0147174
M_u-Ig_t	0.0001787
M_u-Ig_u	0.0004027
M_u-Ir_t	0.0000249
M_u-Ir_u	0.0032520
M_u-M_t	0.0772396
M_u-M_u	0.8934052

estimated_probabilities.k31.txt

kmer size= 31
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 141249232, 'C': 130419484, 'T': 137439145, 'G': 133491423}
state counts= {'Ig_u': 87152, 'Ig_t': 56924, 'Ir_t': 61869, 'Ir_u': 1389091, 'M_u': 175194696, 'M_t': 365809552}
trans counts= {'Ir_t-M_u': 367, 'M_u-Ig_u': 70538, 'M_u-Ig_t': 30884, 'Ig_t-M_u': 461, 'Ig_t-M_t': 43752, 'Ir_t-M_t': 31855, 'Ir_u-M_t': 196867, 'Ir_u-M_u': 367846, 'Ir_t-Ir_t': 28502, 'Ir_t-Ir_u': 645, 'Ig_t-Ig_t': 12281, 'Ig_t-Ig_u': 100, 'Ig_u-M_u': 55509, 'Ig_u-M_t': 11874, 'Ir_u-Ir_u': 819133, 'Ir_u-Ir_t': 4916, 'Ig_u-Ig_u': 15888, 'Ig_u-Ig_t': 3713, 'M_t-Ir_u': 480, 'M_t-Ir_t': 24135, 'M_u-M_u': 156632865, 'M_u-Ir_t': 4316, 'M_u-Ir_u': 568065, 'M_u-M_t': 13335207, 'M_t-Ig_t': 10046, 'M_t-Ig_u': 86, 'M_t-M_t': 352189997, 'M_t-M_u': 5520368}
Ig_t-Ig_t	0.2157438
Ig_t-Ig_u	0.0017567
Ig_t-M_t	0.7686038
Ig_t-M_u	0.0080985
Ig_u-Ig_t	0.0426037
Ig_u-Ig_u	0.1823022
Ig_u-M_t	0.1362447
Ig_u-M_u	0.6369217
Ir_t-Ir_t	0.4606831
Ir_t-Ir_u	0.0104253
Ir_t-M_t	0.5148782
Ir_t-M_u	0.0059319
Ir_u-Ir_t	0.0035390
Ir_u-Ir_u	0.5896899
Ir_u-M_t	0.1417236
Ir_u-M_u	0.2648106
M_t-Ig_t	0.0000275
M_t-Ig_u	0.0000002
M_t-Ir_t	0.0000660
M_t-Ir_u	0.0000013
M_t-M_t	0.9627687
M_t-M_u	0.0150908
M_u-Ig_t	0.0001763
M_u-Ig_u	0.0004026
M_u-Ir_t	0.0000246
M_u-Ir_u	0.0032425
M_u-M_t	0.0761165
M_u-M_u	0.8940503

estimated_probabilities.k32.txt

kmer size= 32
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 137999982, 'C': 127353678, 'T': 134245363, 'G': 130381673}
state counts= {'Ig_u': 87418, 'Ig_t': 56115, 'Ir_t': 60842, 'Ir_u': 1389188, 'M_u': 175565128, 'M_t': 352822005}
trans counts= {'Ir_t-M_u': 347, 'M_u-Ig_u': 70716, 'M_u-Ig_t': 30556, 'Ig_t-M_u': 413, 'Ig_t-M_t': 43154, 'Ir_t-M_t': 31264, 'Ir_u-M_t': 195346, 'Ir_u-M_u': 369368, 'Ir_t-Ir_t': 28226, 'Ir_t-Ir_u': 594, 'Ig_t-Ig_t': 12130, 'Ig_t-Ig_u': 103, 'Ig_u-M_u': 55815, 'Ig_u-M_t': 11788, 'Ir_u-Ir_u': 819383, 'Ir_u-Ir_t': 4835, 'Ig_u-Ig_u': 15977, 'M_u-M_t': 13190533, 'M_t-Ir_u': 483, 'M_t-Ir_t': 23544, 'M_u-M_u': 157056312, 'M_u-Ir_t': 4237, 'M_u-Ir_u': 568061, 'Ig_u-Ig_t': 3683, 'M_t-Ig_t': 9746, 'M_t-Ig_u': 127, 'M_t-M_t': 339349920, 'M_t-M_u': 5465447}
Ig_t-Ig_t	0.2161632
Ig_t-Ig_u	0.0018355
Ig_t-M_t	0.7690279
Ig_t-M_u	0.0073599
Ig_u-Ig_t	0.0421309
Ig_u-Ig_u	0.1827656
Ig_u-M_t	0.1348464
Ig_u-M_u	0.6384841
Ir_t-Ir_t	0.4639229
Ir_t-Ir_u	0.0097630
Ir_t-M_t	0.5138556
Ir_t-M_u	0.0057033
Ir_u-Ir_t	0.0034805
Ir_u-Ir_u	0.5898287
Ir_u-M_t	0.1406188
Ir_u-M_u	0.2658877
M_t-Ig_t	0.0000276
M_t-Ig_u	0.0000004
M_t-Ir_t	0.0000667
M_t-Ir_u	0.0000014
M_t-M_t	0.9618162
M_t-M_u	0.0154907
M_u-Ig_t	0.0001740
M_u-Ig_u	0.0004028
M_u-Ir_t	0.0000241
M_u-Ir_u	0.0032356
M_u-M_t	0.0751319
M_u-M_u	0.8945758

estimated_probabilities.txt

kmer size= 30
seq count= 12933823 dropped seqs= 315235
base counts= {'A': 144454720, 'C': 133529144, 'T': 140678610, 'G': 136555398}
state counts= {'Ig_u': 86973, 'Ig_t': 57725, 'Ir_t': 62885, 'Ir_u': 1389091, 'M_u': 174651791, 'M_t': 378969407}
trans counts= {'Ir_t-M_u': 373, 'M_u-Ig_u': 70341, 'M_u-Ig_t': 31210, 'Ig_t-M_u': 408, 'Ig_t-M_t': 44419, 'Ir_t-M_t': 32511, 'Ir_u-M_t': 198397, 'Ir_u-M_u': 366430, 'Ir_t-Ir_t': 28819, 'Ir_t-Ir_u': 643, 'Ig_t-Ig_t': 12427, 'Ig_t-Ig_u': 121, 'Ig_u-M_u': 55252, 'Ig_u-M_t': 12010, 'Ir_u-Ir_u': 818966, 'Ir_u-Ir_t': 4949, 'Ig_u-Ig_u': 15783, 'M_u-M_t': 13490036, 'M_t-Ir_u': 620, 'M_t-Ir_t': 24770, 'M_u-M_u': 156034825, 'M_u-Ir_t': 4347, 'M_u-Ir_u': 567966, 'Ig_u-Ig_t': 3742, 'M_t-Ig_t': 10346, 'M_t-Ig_u': 102, 'M_t-M_t': 365192034, 'M_t-M_u': 5577437}
Ig_t-Ig_t	0.2152793
Ig_t-Ig_u	0.0020961
Ig_t-M_t	0.7694933
Ig_t-M_u	0.0070680
Ig_u-Ig_t	0.0430248
Ig_u-Ig_u	0.1814701
Ig_u-M_t	0.1380888
Ig_u-M_u	0.6352776
Ir_t-Ir_t	0.4582810
Ir_t-Ir_u	0.0102250
Ir_t-M_t	0.5169913
Ir_t-M_u	0.0059315
Ir_u-Ir_t	0.0035628
Ir_u-Ir_u	0.5895697
Ir_u-M_t	0.1428251
Ir_u-M_u	0.2637912
M_t-Ig_t	0.0000273
M_t-Ig_u	0.0000003
M_t-Ir_t	0.0000654
M_t-Ir_u	0.0000016
M_t-M_t	0.9636452
M_t-M_u	0.0147174
M_u-Ig_t	0.0001787
M_u-Ig_u	0.0004027
M_u-Ir_t	0.0000249
M_u-Ir_u	0.0032520
M_u-M_t	0.0772396
M_u-M_u	0.8934052

Makefile

KSIZE= 30
HASH_SIZE= 4e8
N_HASHES= 4

all: estimated_probabilities.k$(KSIZE).txt

%.fastq.gz:
        wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172903/SRR172903.fastq.gz
        wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172902/SRR172902.fastq.gz

combined_reads.k$(KSIZE).ht: SRR172902.fastq.gz SRR172903.fastq.gz
        load-into-counting.py --ksize $(KSIZE) -x $(HASH_SIZE) -N $(N_HASHES) $@ $^ |& tee combined_reads.k$(KSIZE).log

combined_reads_mapping.bam: SRR172902.fastq.gz SRR172903.fastq.gz
        bowtie2 -x mockRefG -U SRR172902.fastq.gz -U SRR172903.fastq.gz | samtools view -S -F4 -b - > combined_reads_mapping.bam

estimated_probabilities.k$(KSIZE).txt: combined_reads.k$(KSIZE).ht combined_reads_mapping.bam
        python learn.py combined_reads.k$(KSIZE).ht combined_reads_mapping.bam > estimated_probabilities.k$(KSIZE).txt

training-diff-ksizes.ipynb