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table of dn/ds values seem odd #24

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carandraug opened this issue Dec 9, 2015 · 9 comments
Open

table of dn/ds values seem odd #24

carandraug opened this issue Dec 9, 2015 · 9 comments
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@carandraug

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@carandraug
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Values on the table of dn/ds values seem odd. I'm to geta list of dn, ds, and omega values for each each H2A pair to seee what's going on. Andrew to review it.
carandraug added a commit that referenced this issue Dec 13, 2015
@carandraug
pairwise_dn_sd: leave some notes for debuging in the future (issue #24)
907ac2f
carandraug added a commit that referenced this issue Dec 13, 2015
@carandraug
pairwise_dnds: fix too low values of dn/ds due to zero values (issue #24
2576eae 
)

When the sequences were the same, both dN and dS would be zero and dn/ds
ratio would be 99.  The 99 value would shift the mean dn/ds value which
would become too high.
@carandraug
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I think this is fixed now. The issue was, I think, when two sequences were equal, therefore with a dN and dS of zeros. I have solved this by skipping those pairs. Still if you want to inspect this better, here's the pairwise values:

H2A
NP_003503   NP_003500   0.0070  1.0668  0.00658
NP_003503   NP_003502   0.0070  0.7855  0.00895
NP_003503   NP_066390   0.0072  1.1952  0.00605
NP_003503   NP_254280   0.0047  4.6714  0.00100
NP_003503   NP_734466   0.0431  1.6503  0.02610
NP_003503   NP_066409   0.0105  1.6054  0.00656
NP_003503   NP_003505   0.0072  1.1699  0.00612
NP_003503   NP_003504   0.0072  1.3729  0.00526
NP_003503   NP_003507   0.0068  1.3316  0.00514
NP_003503   NP_778235   0.0177  1.5480  0.01143
NP_003503   NP_001035807    0.0068  1.3316  0.00514
NP_003503   NP_003501   0.0070  0.9475  0.00742
NP_003503   NP_542163   0.0072  1.2746  0.00568
NP_003503   NP_066544   0.0107  1.0767  0.00997
NP_003503   NP_066408   0.0071  1.2841  0.00551
NP_003503   NP_003508   0.0069  1.8881  0.00366
NP_003500   NP_003502   0.0007  0.7058  0.00100
NP_003500   NP_066390   0.0073  2.1779  0.00333
NP_003500   NP_254280   0.0098  2.6225  0.00373
NP_003500   NP_734466   0.0514  2.1916  0.02347
NP_003500   NP_066409   0.0034  3.3923  0.00102
NP_003500   NP_003505   0.0013  1.2915  0.00100
NP_003500   NP_003504   0.0071  1.5641  0.00454
NP_003500   NP_003507   0.0067  1.1550  0.00578
NP_003500   NP_778235   0.0250  24.9720 0.00100
NP_003500   NP_001035807    0.0067  1.1550  0.00578
NP_003500   NP_003501   0.0008  0.7701  0.00100
NP_003500   NP_542163   0.0007  0.6757  0.00100
NP_003500   NP_066544   0.0034  0.0783  0.04353
NP_003500   NP_066408   0.0005  0.5403  0.00100
NP_003500   NP_003508   0.0067  1.3957  0.00481
NP_003502   NP_066390   0.0073  4.4333  0.00165
NP_003502   NP_254280   0.0097  2.1900  0.00444
NP_003502   NP_734466   0.0517  2.5262  0.02047
NP_003502   NP_066409   0.0034  1.1133  0.00304
NP_003502   NP_003505   0.0009  0.8600  0.00100
NP_003502   NP_003504   0.0072  2.3046  0.00312
NP_003502   NP_003507   0.0067  2.1480  0.00314
NP_003502   NP_778235   0.0248  2.5320  0.00978
NP_003502   NP_001035807    0.0067  2.1481  0.00314
NP_003502   NP_003501   0.0006  0.6331  0.00100
NP_003502   NP_542163   0.0008  0.8005  0.00100
NP_003502   NP_066544   0.0034  0.9286  0.00368
NP_003502   NP_066408   0.0007  0.6904  0.00100
NP_003502   NP_003508   0.0068  2.3722  0.00285
NP_066390   NP_254280   0.0048  4.8286  0.00100
NP_066390   NP_734466   0.0520  2.5126  0.02069
NP_066390   NP_066409   0.0056  5.5691  0.00100
NP_066390   NP_003505   0.0074  2.7229  0.00273
NP_066390   NP_003504   0.0023  2.2531  0.00100
NP_066390   NP_003507   0.0140  2.0525  0.00681
NP_066390   NP_778235   0.0254  25.4269 0.00100
NP_066390   NP_001035807    0.0140  2.0525  0.00681
NP_066390   NP_003501   0.0072  1.0225  0.00700
NP_066390   NP_542163   0.0074  2.1327  0.00349
NP_066390   NP_066544   0.0111  2.2413  0.00495
NP_066390   NP_066408   0.0074  3.7567  0.00196
NP_066390   NP_003508   0.0141  4.3869  0.00322
NP_254280   NP_734466   0.0438  43.8215 0.00100
NP_254280   NP_066409   0.0065  2.5678  0.00252
NP_254280   NP_003505   0.0115  11.5450 0.00100
NP_254280   NP_003504   0.0034  3.0079  0.00112
NP_254280   NP_003507   0.0097  2.1287  0.00454
NP_254280   NP_778235   0.0199  3.7743  0.00526
NP_254280   NP_001035807    0.0097  2.1287  0.00454
NP_254280   NP_003501   0.0099  3.9226  0.00251
NP_254280   NP_542163   0.0100  2.4615  0.00406
NP_254280   NP_066544   0.0133  3.0884  0.00430
NP_254280   NP_066408   0.0098  2.7090  0.00360
NP_254280   NP_003508   0.0097  3.7886  0.00255
NP_734466   NP_066409   0.0547  3.0921  0.01771
NP_734466   NP_003505   0.0524  2.7967  0.01875
NP_734466   NP_003504   0.0507  1.8888  0.02685
NP_734466   NP_003507   0.0495  7.1457  0.00693
NP_734466   NP_778235   0.0387  38.6652 0.00100
NP_734466   NP_001035807    0.0495  7.1456  0.00693
NP_734466   NP_003501   0.0516  3.3730  0.01530
NP_734466   NP_542163   0.0522  2.8871  0.01809
NP_734466   NP_066544   0.0473  2.1876  0.02163
NP_734466   NP_066408   0.0519  1.8821  0.02758
NP_734466   NP_003508   0.0495  49.5390 0.00100
NP_066409   NP_003505   0.0035  1.2694  0.00275
NP_066409   NP_003504   0.0037  3.7290  0.00100
NP_066409   NP_003507   0.0100  1.9172  0.00521
NP_066409   NP_778235   0.0276  4.4337  0.00622
NP_066409   NP_001035807    0.0100  1.9172  0.00521
NP_066409   NP_003501   0.0034  1.1952  0.00285
NP_066409   NP_542163   0.0035  1.3781  0.00254
NP_066409   NP_066544   0.0070  3.5585  0.00198
NP_066409   NP_066408   0.0034  1.1812  0.00288
NP_066409   NP_003508   0.0101  2.5598  0.00394
NP_003505   NP_003504   0.0073  2.3898  0.00307
NP_003505   NP_003507   0.0069  1.5689  0.00437
NP_003505   NP_778235   0.0247  24.6517 0.00100
NP_003505   NP_001035807    0.0069  1.5689  0.00437
NP_003505   NP_003501   0.0007  0.7186  0.00100
NP_003505   NP_542163   0.0015  1.5462  0.00100
NP_003505   NP_066544   0.0035  1.2073  0.00292
NP_003505   NP_066408   0.0017  1.7020  0.00100
NP_003505   NP_003508   0.0068  1.4654  0.00467
NP_003504   NP_003507   0.0140  2.7166  0.00514
NP_003504   NP_778235   0.0249  24.9494 0.00100
NP_003504   NP_001035807    0.0140  2.7165  0.00514
NP_003504   NP_003501   0.0071  1.2981  0.00544
NP_003504   NP_542163   0.0072  1.0704  0.00672
NP_003504   NP_066544   0.0108  1.3182  0.00817
NP_003504   NP_066408   0.0071  1.2309  0.00579
NP_003504   NP_003508   0.0140  2.1347  0.00658
NP_003507   NP_778235   0.0243  1.2031  0.02022
NP_003507   NP_001035807    0.0000  0.0000  99.00000
NP_003507   NP_003501   0.0067  2.6227  0.00255
NP_003507   NP_542163   0.0068  1.2356  0.00551
NP_003507   NP_066544   0.0101  1.1967  0.00845
NP_003507   NP_066408   0.0067  1.4632  0.00460
NP_003507   NP_003508   0.0003  0.2957  0.00100
NP_778235   NP_001035807    0.0243  1.2031  0.02022
NP_778235   NP_003501   0.0246  3.1224  0.00787
NP_778235   NP_542163   0.0250  3.2715  0.00763
NP_778235   NP_066544   0.0287  28.7392 0.00100
NP_778235   NP_066408   0.0251  25.1156 0.00100
NP_778235   NP_003508   0.0245  1.1084  0.02206
NP_001035807    NP_003501   0.0067  2.6229  0.00255
NP_001035807    NP_542163   0.0068  1.2356  0.00551
NP_001035807    NP_066544   0.0101  1.1967  0.00845
NP_001035807    NP_066408   0.0067  1.4632  0.00460
NP_001035807    NP_003508   0.0003  0.2957  0.00100
NP_003501   NP_542163   0.0007  0.6629  0.00100
NP_003501   NP_066544   0.0034  0.6719  0.00509
NP_003501   NP_066408   0.0008  0.8408  0.00100
NP_003501   NP_003508   0.0067  2.5180  0.00267
NP_542163   NP_066544   0.0035  0.6497  0.00543
NP_542163   NP_066408   0.0007  0.6673  0.00100
NP_542163   NP_003508   0.0068  1.4114  0.00485
NP_066544   NP_066408   0.0034  0.6276  0.00547
NP_066544   NP_003508   0.0102  1.2229  0.00837
NP_066408   NP_003508   0.0067  1.6130  0.00418

H2B
NP_003509   NP_003513   0.0012  1.1637  0.00100
NP_003509   NP_619790   0.0034  1.2867  0.00263
NP_003509   NP_066407   0.0034  1.2867  0.00263
NP_003509   NP_066406   0.0109  1.6726  0.00655
NP_003509   NP_003511   0.0034  2.8628  0.00118
NP_003509   NP_003510   0.0071  7.0559  0.00100
NP_003509   NP_733759   0.0837  2.5601  0.03268
NP_003509   NP_003518   0.0070  2.2463  0.00310
NP_003509   NP_003517   0.0010  0.9726  0.00100
NP_003509   NP_003512   0.0147  3.8259  0.00383
NP_003509   NP_778225   0.0207  2.7314  0.00758
NP_003509   NP_542160   0.0034  2.0749  0.00163
NP_003509   NP_001299582    0.0034  2.0748  0.00163
NP_003509   NP_001019770    0.0066  1.7176  0.00383
NP_003509   NP_001154806    0.0066  1.7177  0.00383
NP_003509   NP_003519   0.0043  4.2699  0.00100
NP_003509   NP_003515   0.0035  2.1105  0.00167
NP_003509   NP_066402   0.0070  1.8088  0.00386
NP_003509   NP_003516   0.0013  1.3293  0.00100
NP_003509   NP_003514   0.0015  1.5017  0.00100
NP_003513   NP_619790   0.0032  0.7090  0.00457
NP_003513   NP_066407   0.0032  0.7090  0.00457
NP_003513   NP_066406   0.0103  0.9353  0.01107
NP_003513   NP_003511   0.0032  1.2042  0.00266
NP_003513   NP_003510   0.0064  4.8598  0.00131
NP_003513   NP_733759   0.0823  3.2829  0.02508
NP_003513   NP_003518   0.0066  0.8765  0.00750
NP_003513   NP_003517   0.0019  1.9443  0.00100
NP_003513   NP_003512   0.0141  4.2524  0.00331
NP_003513   NP_778225   0.0196  1.4193  0.01378
NP_003513   NP_542160   0.0032  0.9685  0.00328
NP_003513   NP_001299582    0.0032  0.9685  0.00328
NP_003513   NP_001019770    0.0063  1.0419  0.00604
NP_003513   NP_001154806    0.0063  1.0419  0.00604
NP_003513   NP_003519   0.0032  1.1291  0.00281
NP_003513   NP_003515   0.0033  0.9866  0.00337
NP_003513   NP_066402   0.0067  1.3773  0.00484
NP_003513   NP_003516   0.0009  0.8785  0.00100
NP_003513   NP_003514   0.0011  1.0892  0.00100
NP_619790   NP_066407   0.0000  0.0000  0.00100
NP_619790   NP_066406   0.0100  1.0882  0.00924
NP_619790   NP_003511   0.0031  0.7918  0.00395
NP_619790   NP_003510   0.0094  0.7243  0.01293
NP_619790   NP_733759   0.0812  5.2375  0.01551
NP_619790   NP_003518   0.0097  1.1081  0.00871
NP_619790   NP_003517   0.0032  0.7166  0.00453
NP_619790   NP_003512   0.0168  0.9976  0.01684
NP_619790   NP_778225   0.0191  1.9309  0.00991
NP_619790   NP_542160   0.0063  1.0923  0.00578
NP_619790   NP_001299582    0.0063  1.0923  0.00578
NP_619790   NP_001019770    0.0094  1.8493  0.00507
NP_619790   NP_001154806    0.0094  1.8492  0.00507
NP_619790   NP_003519   0.0063  1.4967  0.00421
NP_619790   NP_003515   0.0065  1.1829  0.00552
NP_619790   NP_066402   0.0097  0.9294  0.01043
NP_619790   NP_003516   0.0032  0.7376  0.00436
NP_619790   NP_003514   0.0032  0.9791  0.00324
NP_066407   NP_066406   0.0100  1.0882  0.00924
NP_066407   NP_003511   0.0031  0.7918  0.00395
NP_066407   NP_003510   0.0094  0.7243  0.01293
NP_066407   NP_733759   0.0812  5.2374  0.01551
NP_066407   NP_003518   0.0097  1.1080  0.00871
NP_066407   NP_003517   0.0032  0.7166  0.00453
NP_066407   NP_003512   0.0168  0.9976  0.01684
NP_066407   NP_778225   0.0191  1.9309  0.00991
NP_066407   NP_542160   0.0063  1.0923  0.00578
NP_066407   NP_001299582    0.0063  1.0923  0.00578
NP_066407   NP_001019770    0.0094  1.8492  0.00507
NP_066407   NP_001154806    0.0094  1.8492  0.00507
NP_066407   NP_003519   0.0063  1.4967  0.00421
NP_066407   NP_003515   0.0065  1.1830  0.00552
NP_066407   NP_066402   0.0097  0.9294  0.01043
NP_066407   NP_003516   0.0032  0.7376  0.00436
NP_066407   NP_003514   0.0032  0.9791  0.00324
NP_066406   NP_003511   0.0075  7.5326  0.00100
NP_066406   NP_003510   0.0168  2.4598  0.00682
NP_066406   NP_733759   0.0805  3.3240  0.02421
NP_066406   NP_003518   0.0103  1.2480  0.00824
NP_066406   NP_003517   0.0105  1.8934  0.00553
NP_066406   NP_003512   0.0179  1.3237  0.01352
NP_066406   NP_778225   0.0168  1.5578  0.01078
NP_066406   NP_542160   0.0136  1.6909  0.00805
NP_066406   NP_001299582    0.0136  1.6909  0.00805
NP_066406   NP_001019770    0.0169  2.4353  0.00695
NP_066406   NP_001154806    0.0169  2.4352  0.00695
NP_066406   NP_003519   0.0067  1.4265  0.00473
NP_066406   NP_003515   0.0138  0.9874  0.01400
NP_066406   NP_066402   0.0103  1.0941  0.00938
NP_066406   NP_003516   0.0105  1.4550  0.00719
NP_066406   NP_003514   0.0102  1.6849  0.00606
NP_003511   NP_003510   0.0091  0.8374  0.01088
NP_003511   NP_733759   0.0763  5.0200  0.01520
NP_003511   NP_003518   0.0095  0.8861  0.01068
NP_003511   NP_003517   0.0032  1.0196  0.00311
NP_003511   NP_003512   0.0166  2.2528  0.00736
NP_003511   NP_778225   0.0157  1.7059  0.00918
NP_003511   NP_542160   0.0062  1.0803  0.00571
NP_003511   NP_001299582    0.0062  1.0803  0.00571
NP_003511   NP_001019770    0.0092  1.2974  0.00712
NP_003511   NP_001154806    0.0092  1.2974  0.00712
NP_003511   NP_003519   0.0062  1.2040  0.00513
NP_003511   NP_003515   0.0064  1.1373  0.00559
NP_003511   NP_066402   0.0096  1.5056  0.00639
NP_003511   NP_003516   0.0032  1.0739  0.00294
NP_003511   NP_003514   0.0031  0.9529  0.00325
NP_003510   NP_733759   0.0754  4.5200  0.01668
NP_003510   NP_003518   0.0125  1.0987  0.01136
NP_003510   NP_003517   0.0063  0.8591  0.00734
NP_003510   NP_003512   0.0197  1.5323  0.01286
NP_003510   NP_778225   0.0187  2.8043  0.00665
NP_003510   NP_542160   0.0092  1.0793  0.00850
NP_003510   NP_001299582    0.0092  1.0793  0.00850
NP_003510   NP_001019770    0.0122  2.0145  0.00605
NP_003510   NP_001154806    0.0122  2.0145  0.00605
NP_003510   NP_003519   0.0092  1.5161  0.00606
NP_003510   NP_003515   0.0095  1.5498  0.00614
NP_003510   NP_066402   0.0127  1.3720  0.00923
NP_003510   NP_003516   0.0063  0.8675  0.00722
NP_003510   NP_003514   0.0061  0.9742  0.00629
NP_733759   NP_003518   0.0808  2.0093  0.04022
NP_733759   NP_003517   0.0804  2.0774  0.03873
NP_733759   NP_003512   0.0888  2.6399  0.03364
NP_733759   NP_778225   0.0806  6.1137  0.01318
NP_733759   NP_542160   0.0851  3.7462  0.02273
NP_733759   NP_001299582    0.0851  3.7462  0.02272
NP_733759   NP_001019770    0.0882  4.9000  0.01801
NP_733759   NP_001154806    0.0882  4.9000  0.01801
NP_733759   NP_003519   0.0762  4.8703  0.01564
NP_733759   NP_003515   0.0876  3.5777  0.02450
NP_733759   NP_066402   0.0817  4.0165  0.02033
NP_733759   NP_003516   0.0819  4.9367  0.01659
NP_733759   NP_003514   0.0808  4.6008  0.01757
NP_003518   NP_003517   0.0065  0.9142  0.00712
NP_003518   NP_003512   0.0202  1.0948  0.01849
NP_003518   NP_778225   0.0128  1.2484  0.01025
NP_003518   NP_542160   0.0095  0.9987  0.00949
NP_003518   NP_001299582    0.0095  0.9987  0.00949
NP_003518   NP_001019770    0.0063  1.5581  0.00403
NP_003518   NP_001154806    0.0063  1.5581  0.00403
NP_003518   NP_003519   0.0031  0.8189  0.00381
NP_003518   NP_003515   0.0033  1.3726  0.00239
NP_003518   NP_066402   0.0066  1.4036  0.00467
NP_003518   NP_003516   0.0065  1.5174  0.00431
NP_003518   NP_003514   0.0064  1.0706  0.00594
NP_003517   NP_003512   0.0135  1.0707  0.01264
NP_003517   NP_778225   0.0196  2.2082  0.00886
NP_003517   NP_542160   0.0032  1.3339  0.00240
NP_003517   NP_001299582    0.0032  1.3339  0.00240
NP_003517   NP_001019770    0.0063  1.4335  0.00440
NP_003517   NP_001154806    0.0063  1.4335  0.00440
NP_003517   NP_003519   0.0032  1.2291  0.00258
NP_003517   NP_003515   0.0033  1.1286  0.00295
NP_003517   NP_066402   0.0066  1.0188  0.00649
NP_003517   NP_003516   0.0010  0.9562  0.00100
NP_003517   NP_003514   0.0007  0.7450  0.00100
NP_003512   NP_778225   0.0342  3.2706  0.01044
NP_003512   NP_542160   0.0166  1.3808  0.01205
NP_003512   NP_001299582    0.0166  1.3808  0.01205
NP_003512   NP_001019770    0.0198  1.8513  0.01067
NP_003512   NP_001154806    0.0198  1.8513  0.01067
NP_003512   NP_003519   0.0165  1.3833  0.01194
NP_003512   NP_003515   0.0173  1.7035  0.01018
NP_003512   NP_066402   0.0205  1.6580  0.01233
NP_003512   NP_003516   0.0135  1.1202  0.01208
NP_003512   NP_003514   0.0134  1.6227  0.00829
NP_778225   NP_542160   0.0223  2.2649  0.00984
NP_778225   NP_001299582    0.0223  2.2648  0.00984
NP_778225   NP_001019770    0.0190  0.9193  0.02065
NP_778225   NP_001154806    0.0190  0.9192  0.02065
NP_778225   NP_003519   0.0157  1.1483  0.01366
NP_778225   NP_003515   0.0166  5.0245  0.00330
NP_778225   NP_066402   0.0196  2.0411  0.00960
NP_778225   NP_003516   0.0195  1.8794  0.01038
NP_778225   NP_003514   0.0191  2.3461  0.00814
NP_542160   NP_001299582    0.0000  0.0000  99.00000
NP_542160   NP_001019770    0.0093  1.0057  0.00920
NP_542160   NP_001154806    0.0093  1.0057  0.00920
NP_542160   NP_003519   0.0062  1.0924  0.00567
NP_542160   NP_003515   0.0064  0.9652  0.00664
NP_542160   NP_066402   0.0032  0.8635  0.00369
NP_542160   NP_003516   0.0032  1.1185  0.00285
NP_542160   NP_003514   0.0031  0.6646  0.00468
NP_001299582    NP_001019770    0.0093  1.0057  0.00920
NP_001299582    NP_001154806    0.0093  1.0057  0.00920
NP_001299582    NP_003519   0.0062  1.0924  0.00567
NP_001299582    NP_003515   0.0064  0.9652  0.00664
NP_001299582    NP_066402   0.0032  0.8635  0.00369
NP_001299582    NP_003516   0.0032  1.1185  0.00285
NP_001299582    NP_003514   0.0031  0.6646  0.00468
NP_001019770    NP_001154806    0.0000  0.0000  99.00000
NP_001019770    NP_003519   0.0093  0.5717  0.01625
NP_001019770    NP_003515   0.0032  1.6845  0.00187
NP_001019770    NP_066402   0.0128  1.7694  0.00723
NP_001019770    NP_003516   0.0063  1.5758  0.00400
NP_001019770    NP_003514   0.0062  1.2514  0.00495
NP_001154806    NP_003519   0.0093  0.5717  0.01625
NP_001154806    NP_003515   0.0032  1.6845  0.00187
NP_001154806    NP_066402   0.0128  1.7694  0.00723
NP_001154806    NP_003516   0.0063  1.5758  0.00400
NP_001154806    NP_003514   0.0062  1.2514  0.00495
NP_003519   NP_003515   0.0063  1.6482  0.00384
NP_003519   NP_066402   0.0032  1.4525  0.00219
NP_003519   NP_003516   0.0032  1.2809  0.00248
NP_003519   NP_003514   0.0031  1.2143  0.00255
NP_003515   NP_066402   0.0099  0.9425  0.01049
NP_003515   NP_003516   0.0033  0.9231  0.00357
NP_003515   NP_003514   0.0032  0.5234  0.00614
NP_066402   NP_003516   0.0066  1.0580  0.00623
NP_066402   NP_003514   0.0064  1.0344  0.00621
NP_003516   NP_003514   0.0009  0.9257  0.00100

H3
NP_066298   NP_003484   0.0129  2.4835  0.00519
NP_066298   NP_003527   0.0024  2.4469  0.00100
NP_066298   NP_003522   0.0035  3.5119  0.00100
NP_066298   NP_003526   0.0015  1.4865  0.00100
NP_066298   NP_003520   0.0012  1.2341  0.00100
NP_066298   NP_003525   0.0012  1.1936  0.00100
NP_066298   NP_003524   0.0011  1.1106  0.00100
NP_066298   NP_003528   0.0015  1.5484  0.00100
NP_066298   NP_001005464    0.0034  3.4244  0.00100
NP_066298   NP_003521   0.0010  0.9833  0.00100
NP_066298   NP_066403   0.0034  3.4244  0.00100
NP_066298   NP_003523   0.0028  2.7651  0.00100
NP_066298   NP_001116847    0.0038  3.8440  0.00100
NP_003484   NP_003527   0.0124  3.9520  0.00315
NP_003484   NP_003522   0.0133  5.8794  0.00226
NP_003484   NP_003526   0.0130  3.4445  0.00378
NP_003484   NP_003520   0.0130  2.2309  0.00582
NP_003484   NP_003525   0.0127  1.8826  0.00677
NP_003484   NP_003524   0.0125  1.4067  0.00888
NP_003484   NP_003528   0.0132  3.9299  0.00336
NP_003484   NP_001005464    0.0149  2.5588  0.00580
NP_003484   NP_003521   0.0127  2.8470  0.00445
NP_003484   NP_066403   0.0149  2.5588  0.00580
NP_003484   NP_003523   0.0130  5.9806  0.00217
NP_003484   NP_001116847    0.0148  2.4591  0.00601
NP_003527   NP_003522   0.0038  3.7558  0.00100
NP_003527   NP_003526   0.0032  3.1686  0.00100
NP_003527   NP_003520   0.0029  2.9348  0.00100
NP_003527   NP_003525   0.0030  3.0205  0.00100
NP_003527   NP_003524   0.0016  1.5793  0.00100
NP_003527   NP_003528   0.0029  2.8640  0.00100
NP_003527   NP_001005464    0.0042  4.2445  0.00100
NP_003527   NP_003521   0.0018  1.8118  0.00100
NP_003527   NP_066403   0.0042  4.2445  0.00100
NP_003527   NP_003523   0.0022  2.1819  0.00100
NP_003527   NP_001116847    0.0047  4.7049  0.00100
NP_003522   NP_003526   0.0013  1.3488  0.00100
NP_003522   NP_003520   0.0028  2.8254  0.00100
NP_003522   NP_003525   0.0036  3.5934  0.00100
NP_003522   NP_003524   0.0012  1.1747  0.00100
NP_003522   NP_003528   0.0013  1.2509  0.00100
NP_003522   NP_001005464    0.0031  2.3880  0.00132
NP_003522   NP_003521   0.0026  2.6174  0.00100
NP_003522   NP_066403   0.0031  2.3881  0.00132
NP_003522   NP_003523   0.0010  0.9762  0.00100
NP_003522   NP_001116847    0.0031  2.4006  0.00131
NP_003526   NP_003520   0.0017  1.6780  0.00100
NP_003526   NP_003525   0.0020  2.0130  0.00100
NP_003526   NP_003524   0.0017  1.7037  0.00100
NP_003526   NP_003528   0.0033  3.2668  0.00100
NP_003526   NP_001005464    0.0048  4.8237  0.00100
NP_003526   NP_003521   0.0031  3.1427  0.00100
NP_003526   NP_066403   0.0031  3.1124  0.00100
NP_003526   NP_003523   0.0026  2.6364  0.00100
NP_003526   NP_001116847    0.0049  4.9314  0.00100
NP_003520   NP_003525   0.0017  1.6759  0.00100
NP_003520   NP_003524   0.0016  1.6399  0.00100
NP_003520   NP_003528   0.0016  1.5803  0.00100
NP_003520   NP_001005464    0.0031  1.9993  0.00157
NP_003520   NP_003521   0.0015  1.5087  0.00100
NP_003520   NP_066403   0.0031  1.9994  0.00157
NP_003520   NP_003523   0.0029  2.8976  0.00100
NP_003520   NP_001116847    0.0031  2.6735  0.00117
NP_003525   NP_003524   0.0030  2.9624  0.00100
NP_003525   NP_003528   0.0011  1.1276  0.00100
NP_003525   NP_001005464    0.0043  4.3134  0.00100
NP_003525   NP_003521   0.0010  0.9972  0.00100
NP_003525   NP_066403   0.0043  4.3134  0.00100
NP_003525   NP_003523   0.0013  1.2683  0.00100
NP_003525   NP_001116847    0.0044  4.3859  0.00100
NP_003524   NP_003528   0.0014  1.4033  0.00100
NP_003524   NP_001005464    0.0030  1.7461  0.00173
NP_003524   NP_003521   0.0012  1.1861  0.00100
NP_003524   NP_066403   0.0030  1.7460  0.00174
NP_003524   NP_003523   0.0009  0.9386  0.00100
NP_003524   NP_001116847    0.0030  2.5157  0.00120
NP_003528   NP_001005464    0.0032  2.7606  0.00114
NP_003528   NP_003521   0.0009  0.9470  0.00100
NP_003528   NP_066403   0.0032  2.7601  0.00114
NP_003528   NP_003523   0.0011  1.1283  0.00100
NP_003528   NP_001116847    0.0035  3.5120  0.00100
NP_001005464    NP_003521   0.0032  3.2451  0.00100
NP_001005464    NP_066403   0.0000  0.0000  0.10752
NP_001005464    NP_003523   0.0031  2.9723  0.00104
NP_001005464    NP_001116847    0.0004  0.4151  0.00100
NP_003521   NP_066403   0.0032  3.2451  0.00100
NP_003521   NP_003523   0.0014  1.4390  0.00100
NP_003521   NP_001116847    0.0035  3.5052  0.00100
NP_066403   NP_003523   0.0031  2.9711  0.00104
NP_066403   NP_001116847    0.0004  0.4151  0.00100
NP_003523   NP_001116847    0.0031  2.2197  0.00138

H4
NP_778224   NP_003532   0.0033  3.2818  0.00100
NP_778224   NP_003537   0.0024  2.3933  0.00100
NP_778224   NP_003486   0.0019  1.9435  0.00100
NP_778224   NP_003530   0.0019  1.8869  0.00100
NP_778224   NP_003535   0.0038  3.7798  0.00100
NP_778224   NP_001029249    0.0035  3.5090  0.00100
NP_778224   NP_003539   0.0035  3.5090  0.00100
NP_778224   NP_003531   0.0035  3.4647  0.00100
NP_778224   NP_003536   0.0017  1.6924  0.00100
NP_778224   NP_068803   0.0033  3.2818  0.00100
NP_778224   NP_003538   0.0774  3.2359  0.02393
NP_778224   NP_003533   0.0045  4.4563  0.00100
NP_778224   NP_003529   0.0021  2.1174  0.00100
NP_778224   NP_003534   0.0023  2.3224  0.00100
NP_003532   NP_003537   0.0015  1.5024  0.00100
NP_003532   NP_003486   0.0013  1.3183  0.00100
NP_003532   NP_003530   0.0035  3.5483  0.00100
NP_003532   NP_003535   0.0033  3.2621  0.00100
NP_003532   NP_001029249    0.0064  6.3871  0.00100
NP_003532   NP_003539   0.0064  6.3871  0.00100
NP_003532   NP_003531   0.0043  4.3053  0.00100
NP_003532   NP_003536   0.0016  1.5820  0.00100
NP_003532   NP_068803   0.0000  0.0000  0.00100
NP_003532   NP_003538   0.0783  1.4109  0.05549
NP_003532   NP_003533   0.0037  3.6653  0.00100
NP_003532   NP_003529   0.0027  2.6924  0.00100
NP_003532   NP_003534   0.0029  2.9260  0.00100
NP_003537   NP_003486   0.0013  1.3229  0.00100
NP_003537   NP_003530   0.0016  1.5533  0.00100
NP_003537   NP_003535   0.0020  1.9668  0.00100
NP_003537   NP_001029249    0.0039  3.9093  0.00100
NP_003537   NP_003539   0.0039  3.9093  0.00100
NP_003537   NP_003531   0.0034  3.4398  0.00100
NP_003537   NP_003536   0.0013  1.2697  0.00100
NP_003537   NP_068803   0.0015  1.5024  0.00100
NP_003537   NP_003538   0.0817  1.9597  0.04171
NP_003537   NP_003533   0.0035  3.5058  0.00100
NP_003537   NP_003529   0.0015  1.4671  0.00100
NP_003537   NP_003534   0.0024  2.3695  0.00100
NP_003486   NP_003530   0.0020  2.0342  0.00100
NP_003486   NP_003535   0.0035  3.5232  0.00100
NP_003486   NP_001029249    0.0023  2.2712  0.00100
NP_003486   NP_003539   0.0023  2.2712  0.00100
NP_003486   NP_003531   0.0029  2.8918  0.00100
NP_003486   NP_003536   0.0018  1.8130  0.00100
NP_003486   NP_068803   0.0013  1.3183  0.00100
NP_003486   NP_003538   0.0750  1.4448  0.05191
NP_003486   NP_003533   0.0050  4.9557  0.00100
NP_003486   NP_003529   0.0035  3.4834  0.00100
NP_003486   NP_003534   0.0017  1.7388  0.00100
NP_003530   NP_003535   0.0028  2.7868  0.00100
NP_003530   NP_001029249    0.0021  2.1195  0.00100
NP_003530   NP_003539   0.0021  2.1195  0.00100
NP_003530   NP_003531   0.0018  1.8473  0.00100
NP_003530   NP_003536   0.0012  1.1680  0.00100
NP_003530   NP_068803   0.0035  3.5483  0.00100
NP_003530   NP_003538   0.0837  1.5216  0.05499
NP_003530   NP_003533   0.0039  3.8728  0.00100
NP_003530   NP_003529   0.0018  1.7717  0.00100
NP_003530   NP_003534   0.0012  1.2357  0.00100
NP_003535   NP_001029249    0.0049  4.9188  0.00100
NP_003535   NP_003539   0.0049  4.9188  0.00100
NP_003535   NP_003531   0.0013  1.3283  0.00100
NP_003535   NP_003536   0.0016  1.5982  0.00100
NP_003535   NP_068803   0.0033  3.2621  0.00100
NP_003535   NP_003538   0.0825  2.1178  0.03895
NP_003535   NP_003533   0.0017  1.6666  0.00100
NP_003535   NP_003529   0.0019  1.9436  0.00100
NP_003535   NP_003534   0.0014  1.3717  0.00100
NP_001029249    NP_003539   0.0000  0.0000  98.99998
NP_001029249    NP_003531   0.0021  2.1121  0.00100
NP_001029249    NP_003536   0.0027  2.7260  0.00100
NP_001029249    NP_068803   0.0064  6.3871  0.00100
NP_001029249    NP_003538   0.0783  1.7087  0.04580
NP_001029249    NP_003533   0.0054  5.3775  0.00100
NP_001029249    NP_003529   0.0028  2.7672  0.00100
NP_001029249    NP_003534   0.0017  1.7492  0.00100
NP_003539   NP_003531   0.0021  2.1121  0.00100
NP_003539   NP_003536   0.0027  2.7260  0.00100
NP_003539   NP_068803   0.0064  6.3871  0.00100
NP_003539   NP_003538   0.0783  1.7087  0.04580
NP_003539   NP_003533   0.0054  5.3775  0.00100
NP_003539   NP_003529   0.0028  2.7672  0.00100
NP_003539   NP_003534   0.0017  1.7492  0.00100
NP_003531   NP_003536   0.0039  3.8604  0.00100
NP_003531   NP_068803   0.0043  4.3053  0.00100
NP_003531   NP_003538   0.0816  1.2820  0.06365
NP_003531   NP_003533   0.0023  2.3122  0.00100
NP_003531   NP_003529   0.0027  2.6645  0.00100
NP_003531   NP_003534   0.0017  1.7456  0.00100
NP_003536   NP_068803   0.0016  1.5820  0.00100
NP_003536   NP_003538   0.0818  3.5022  0.02334
NP_003536   NP_003533   0.0055  5.5495  0.00100
NP_003536   NP_003529   0.0015  1.5282  0.00100
NP_003536   NP_003534   0.0006  0.5908  0.00100
NP_068803   NP_003538   0.0783  1.4109  0.05549
NP_068803   NP_003533   0.0037  3.6653  0.00100
NP_068803   NP_003529   0.0027  2.6924  0.00100
NP_068803   NP_003534   0.0029  2.9260  0.00100
NP_003538   NP_003533   0.0834  2.2240  0.03749
NP_003538   NP_003529   0.0791  1.9338  0.04089
NP_003538   NP_003534   0.0815  3.1971  0.02549
NP_003533   NP_003529   0.0031  3.0721  0.00100
NP_003533   NP_003534   0.0033  3.2573  0.00100
NP_003529   NP_003534   0.0018  1.8335  0.00100

@carandraug
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Close it if you agree this is fixed.

@carandraug
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ping Can I close this?

@aflaus
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aflaus commented Mar 27, 2016

I had a look at this and the values people seem to quote are 10-20x higher. See:

There is possibly some variation by the counting algorithm, and your dN and dS values will be 100x lower because you are per site whereas they are counting events in the sequence (103 aa). It seems you have dN = 0.0134 x 103 = 1.4 which is close enough to their 0.7. However, dS = 2.76 x 103 = 280 which is 5x their value.

I will think some more about this ...

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aflaus commented Mar 27, 2016

I just realised that based on the IDs you seem to have done a NP v NP (protein) comparison. Is that right? Can you please change this to a gene coding region (DNA) based calculation. Should be straightforward?

@carandraug
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I just realised that based on the IDs you seem to have done a NP v NP (protein) comparison. Is that right? Can you please change this to a gene coding region (DNA) based calculation. Should be straightforward?

The calculations were done with the DNA coding sequences. The IDs were of the proteins because the alignment is done in protein space and then the CDS were mapped to it (otherwise the alignment would space 3 nucleotide gaps instead of a single codon gap).

@carandraug carandraug removed their assignment Dec 11, 2016
@aflaus aflaus self-assigned this Dec 15, 2016
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aflaus commented Dec 17, 2016

I sent the manuscript on to Cathal Seoighe to get his feedback

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aflaus commented Dec 22, 2016

I have updated the table S8 legend based on Cathal's feedback. Two additional items to fix in scripts:

  1. In table S8 dN, dS and ration should have 2 significant figures only. Can we apply a rounding function.

  2. In table S9 the amino acids that are not represented should show "NA" and not zero, because they have no denominator. These are Cys in H2A and H2B, Trp in H2A and H3. All the other zeros are ok.

@aflaus aflaus assigned carandraug and unassigned aflaus Dec 22, 2016
carandraug added a commit that referenced this issue Jan 14, 2017
@carandraug
codon_usage.pl: use NA for rel frequency in non-represented aa (issue #…
f138984 
…24)
@carandraug
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In table S8 dN, dS and ration should have 2 significant figures only. Can we apply a rounding function.

Why? Is this due to propagation of rounding errors? Maybe I'm doing it wrong but I think this is more. If mean is a sum of a list and then division by an exact number, then the result should be rounded to the number of significant figures of the sum of the values. The number of significant figures of that sum is dependent on the least significant digit of the series of numbers being summed (and not their number of significant digits).

For example, for H3 dN, the number with least precision is significant to the 1/1000 digit (all the dN numbers are like that). The sum of the dN until that digit is 0.3687. This number has 4 significant digits so after division should be rounded to 4 significant digits and so to 0.004097

And for dS (which has bigger numbers), the sum is 227.8282 which has 7 significant digits so after division with the same number of significant digits is 2.531424.

In table S9 the amino acids that are not represented should show "NA" and not zero, because they have no denominator. These are Cys in H2A and H2B, Trp in H2A and H3. All the other zeros are ok.

Fixed.

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