https://github.com/blab/mumps-wa-phylodynamics
Tip revision: b8358a0d49d70670dbab9eeffa9972c277b3021b authored by Louise Moncla on 17 March 2021, 19:25:20 UTC
adding in callouts for Wisconsin H and A genomes
adding in callouts for Wisconsin H and A genomes
Tip revision: b8358a0
sample-metadata-public-2020-12-10.txt
strain_name sample_collection_date type_sample country US_state genotype vaccination_status Ct percent_genome_coverage
MuVs/Washington.USA/48.16/FH1[G] 2016-12-07 Buccal Swab USA Washington G up_to_date 29.32 0.909
MuVs/Washington.USA/50.16/FH2[G] 2016-12-13 Buccal Swab USA Washington G up_to_date 25.11 0.926
MuVs/Washington.USA/50.16/FH3[G] 2016-12-12 Buccal Swab USA Washington G up_to_date 28.53 0.841
MuVs/Washington.USA/50.16/FH4[G] 2016-12-13 Buccal Swab USA Washington G unknown 27.51 0.841
MuVs/Washington.USA/1.17/FH5[G] 2017-01-03 Buccal Swab USA Washington G up_to_date 23.04 0.926
MuVs/Washington.USA/1.17/FH6[G] 2017-01-04 Buccal Swab USA Washington G not_up_to_date 32.87 0.926
MuVs/Washington.USA/1.17/FH7[G] 2017-01-06 Buccal Swab USA Washington G up_to_date 25.29 0.921
MuVs/Washington.USA/1.17/FH8[G] 2017-01-05 Buccal Swab USA Washington G unknown 26.61 0.926
MuVs/Washington.USA/5.17/FH9[G] 2017-01-31 Buccal Swab USA Washington G up_to_date 30.38 0.841
MuVs/Washington.USA/5.17/FH10[G] 2017-02-04 Buccal Swab USA Washington G up_to_date 26.72 0.919
MuVs/Washington.USA/5.17/FH11[G] 2017-02-08 Buccal Swab USA Washington G up_to_date 28.17 0.926
MuVs/Washington.USA/6.17/FH12[G] 2017-02-08 Buccal Swab USA Washington G unknown 25.00 0.926
MuVs/Washington.USA/6.17/FH13[G] 2017-02-13 Buccal Swab USA Washington G up_to_date 25.31 0.926
MuVs/Washington.USA/6.17/FH14[G] 2017-02-08 Buccal Swab USA Washington G unknown 29.04 0.925
MuVs/Washington.USA/7.17/FH15[G] 2017-02-15 Buccal Swab USA Washington G unknown 33.33 0.923
MuVs/Washington.USA/9.17/FH16[G] 2017-02-28 Buccal Swab USA Washington G up_to_date 23.17 0.926
MuVs/Washington.USA/8.17/FH17[G] 2017-02-23 Buccal Swab USA Washington G up_to_date 28.83 0.919
MuVs/Washington.USA/9.17/FH18[G] 2017-03-01 Buccal Swab USA Washington G up_to_date 31.84 0.841
MuVs/Washington.USA/8.17/FH19[G] 2017-02-28 Buccal Swab USA Washington G unknown 32.16 0.926
MuVs/Washington.USA/15.17/FH20[G] 2017-04-13 Buccal Swab USA Washington G up_to_date 22.25 0.926
MuVs/Washington.USA/2.17/FH21[G] 2017-01-13 Buccal Swab USA Washington G up_to_date 26.50 0.922
MuVs/Washington.USA/2.17/FH22[G] 2017-01-17 Buccal Swab USA Washington G not_up_to_date 31.09 0.854
MuVs/Washington.USA/2.17/FH23[G] 2017-01-13 Buccal Swab USA Washington G up_to_date 25.61 0.92
MuVs/Washington.USA/3.17/FH24[G] 2017-01-19 Buccal Swab USA Washington G up_to_date 21.89 0.926
MuVs/Washington.USA/3.17/FH25[G] 2017-01-20 Buccal Swab USA Washington G up_to_date 27.23 0.925
MuVs/Washington.USA/2.17/FH26[G] 2017-01-12 Buccal Swab USA Washington G up_to_date 29.08 0.926
MuVs/Washington.USA/5.17/FH27[G] 2017-01-30 Buccal Swab USA Washington G up_to_date 24.53 0.926
MuVs/Washington.USA/52.16/FH28[G] 2016-12-31 Buccal Swab USA Washington G unknown 34.28 0.738
MuVs/Washington.USA/1.17/FH29[G] 2017-01-10 Buccal Swab USA Washington G up_to_date 33.14 0.642
MuVs/Washington.USA/5.17/FH30[G] 2017-02-02 Buccal Swab USA Washington G unknown 33.27 0.633
MuVs/Washington.USA/9.17/FH31[G] 2017-03-01 Buccal Swab USA Washington G up_to_date 34.94 0.664
MuVs/Washington.USA/30.17/FH32[G] 2017-07-25 Buccal Swab USA Washington G not_up_to_date 21.88 0.926
MuVs/Washington.USA/50.16/FH33[G] 2016-12-19 Buccal Swab USA Washington G unknown 23.94 0.917
MuVs/Washington.USA/12.17/FH34[G] 2017-03-22 Buccal Swab USA Washington G up_to_date 24.15 0.926
MuVs/Washington.USA/12.17/FH35[G] 2017-03-24 Buccal Swab USA Washington G not_up_to_date 28.12 0.926
MuVs/Washington.USA/16.17/FH36[G] 2017-04-19 Buccal Swab USA Washington G up_to_date 25.15 0.926
MuVs/Washington.USA/17.17/FH37[G] 2017-05-02 Buccal Swab USA Washington G unknown 25.71 0.935
MuVs/Washington.USA/17.17/FH38[G] 2017-04-25 Buccal Swab USA Washington G unknown 26.45 0.926
MuVs/Washington.USA/17.17/FH39[G] 2017-04-27 Buccal Swab USA Washington G up_to_date 26.69 0.926
MuVs/Washington.USA/17.17/FH40[G] 2017-04-29 Buccal Swab USA Washington G up_to_date 21.78 0.926
MuVs/Washington.USA/51.16/FH41[G] 2016-12-21 Buccal Swab USA Washington G unknown 23.56 0.926
MuVs/Washington.USA/9.17/FH42[G] 2017-03-06 Buccal Swab USA Washington G up_to_date 23.29 0.926
MuVs/Washington.USA/10.17/FH43[G] 2017-03-07 Buccal Swab USA Washington G up_to_date 24.50 0.997
MuVs/Washington.USA/19.17/FH44[G] 2017-05-10 Buccal Swab USA Washington G unknown 27.26 0.926
MuVs/Washington.USA/49.16/FH45[G] 2016-12-10 Buccal Swab USA Washington G unknown 30.24 0.926
MuVs/Washington.USA/51.16/FH46[G] 2016-12-22 Buccal Swab USA Washington G unknown 25.69 0.926
MuVs/Washington.USA/2.17/FH47[G] 2017-01-11 Buccal Swab USA Washington G up_to_date 24.04 0.926
MuVs/Washington.USA/4.17/FH48[G] 2017-01-28 Buccal Swab USA Washington G up_to_date 20.15 0.926
MuVs/Washington.USA/4.17/FH49[G] 2017-01-31 Buccal Swab USA Washington G up_to_date 31.31 0.926
MuVs/Washington.USA/5.17/FH50[G] 2017-02-06 Buccal Swab USA Washington G unknown 31.14 0.848
MuVs/Washington.USA/6.17/FH51[G] 2017-02-06 Buccal Swab USA Washington G unknown 26.59 0.919
MuVs/Washington.USA/10.17/FH52[G] 2017-03-12 Buccal Swab USA Washington G not_up_to_date 23.76 0.935
MuVs/Washington.USA/19.17/FH53[G] 2017-05-12 Buccal Swab USA Washington G unknown 22.25 0.926
MuVs/Washington.USA/2.17/FH54[G] 2017-01-12 Buccal Swab USA Washington G up_to_date 24.47 0.842
MuVs/Washington.USA/49.16/FH55[G] 2016-12-07 nasopharyngeal/throat swab USA Washington G unknown 28.39 0.841
MuVs/Washington.USA/11.17/FH56[G] 2017-03-15 Buccal Swab USA Washington G unknown 25.31 0.995
MuVs/Washington.USA/12.17/FH57[G] 2017-03-22 Buccal Swab USA Washington G unknown 32.79 0.926
MuVs/Washington.USA/2.17/FH58[G] 2017-01-13 Buccal Swab USA Washington G up_to_date 23.20 0.926
MuVs/Washington.USA/3.17/FH59[G] 2017-01-18 Buccal Swab USA Washington G up_to_date 26.24 0.926
MuVs/Washington.USA/4.17/FH60[G] 2017-02-03 Buccal Swab USA Washington G not_up_to_date 26.87 0.926
MuVs/Washington.USA/7.17/FH61[G] 2017-02-22 Buccal Swab USA Washington G unknown 24.86 0.978
MuVs/Washington.USA/3.17/FH62[G] 2017-01-19 Buccal Swab USA Washington G unknown 26.99 0.942
MuVs/Washington.USA/16.17/FH63[G] 2017-04-21 Buccal Swab USA Washington G up_to_date 24.26 0.992
MuVs/Washington.USA/50.16/FH64[G] 2016-12-12 Buccal Swab USA Washington G up_to_date 34.54 0.926
MuVs/Washington.USA/1.17/FH65[G] 2017-01-08 Buccal Swab USA Washington G up_to_date 28.53 0.926
MuVs/Washington.USA/2.17/FH66[G] 2017-01-13 Buccal Swab USA Washington G unknown 23.51 0.93
MuVs/Washington.USA/3.17/FH67[G] 2017-01-17 Buccal Swab USA Washington G up_to_date 29.70 0.926
MuVs/Washington.USA/4.17/FH68[G] 2017-01-26 Buccal Swab USA Washington G up_to_date 27.07 0.926
MuVs/Washington.USA/21.17/FH69[G] 2017-05-22 Buccal Swab USA Washington G not_up_to_date 22.46 0.926
MuVs/Washington.USA/4.17/FH70[G] 2017-01-30 Buccal Swab USA Washington G unknown 25.32 0.926
MuVs/Washington.USA/4.17/FH71[G] 2017-01-30 Buccal Swab USA Washington G up_to_date 25.92 0.926
MuVs/Washington.USA/5.17/FH72[G] 2017-02-01 Buccal Swab USA Washington G unknown 22.74 0.926
MuVs/Washington.USA/20.17/FH73[G] 2017-05-21 Buccal Swab USA Washington G up_to_date 28.59 0.926
MuVs/Washington.USA/22.17/FH74[G] 2017-05-30 Buccal Swab USA Washington G up_to_date 28.84 0.926
MuVs/Washington.USA/52.16/FH75[G] 2016-12-30 Buccal Swab USA Washington G up_to_date 27.02 0.926
MuVs/Washington.USA/12.17/FH76[G] 2017-03-22 Buccal Swab USA Washington G not_up_to_date 25.15 0.926
MuVs/Washington.USA/1.17/FH77[G] 2017-01-11 Buccal Swab USA Washington G up_to_date 34.73 0.925
MuVs/Washington.USA/12.17/FH78[G] 2017-03-24 Buccal Swab USA Washington G unknown 27.05 0.896
MuVs/Washington.USA/16.17/FH79[G] 2017-04-23 Buccal Swab USA Washington G up_to_date 27.44 0.926
MuVs/Washington.USA/19.17/FH80[G] 2017-05-11 Buccal Swab USA Washington G unknown 29.00 0.926
MuVs/Washington.USA/20.17/FH81[G] 2017-05-21 Buccal Swab USA Washington G not_up_to_date 27.85 0.926
MuVs/Washington.USA/20.17/FH82[G] 2017-05-22 Buccal Swab USA Washington G up_to_date 33.04 0.841
MuVs/Washington.USA/29.17/FH83[G] 2017-07-26 Buccal Swab USA Washington G not_up_to_date 32.28 0.926
MuVs/Washington.USA/2.17/FH84[G] 2017-01-13 Buccal Swab USA Washington G not_up_to_date 23.08 0.841
MuVs/Wisconsin.USA/16.14/FH85[G] 2014-04 unknown USA Wisconsin G unknown unknown 0.764
MuVs/Wisconsin.USA/20.14/FH86[G] 2014-05 unknown USA Wisconsin G unknown unknown 0.58
MuVs/Wisconsin.USA/15.06/FH87[H] 2006-04 unknown USA Wisconsin H unknown unknown 0.534
MuVs/Missouri.USA/32.16/FH88[G] 2016-08 unknown USA Missouri G unknown unknown 0.776
MuVs/Wisconsin.USA/15.17/FH89[G] 2017-04 unknown USA Wisconsin G unknown unknown 0.784
MuVs/Alabama.USA/11.17/FH90[G] 2017-03 unknown USA Alabama G unknown unknown 0.797
MuVs/Wisconsin.USA/15.06/FH91[A] 2006-04 unknown USA Wisconsin A unknown unknown 0.705
MuVs/Alabama.USA/19.17/FH92[G] 2017-05 unknown USA Alabama G unknown unknown 0.774
MuVs/Wisconsin.USA/37.06/FH93[G] 2006-09 unknown USA Wisconsin G unknown unknown 0.689
MuVs/Washington.USA/9.17/FH94[K] 2017-02-28 Buccal Swab USA Washington K unknown 29.13 0.628
MuVs/Washington.USA/11.17/FH95[G] 2017-03-15 Buccal Swab USA Washington G up_to_date 28.52 0.773
MuVs/Washington.USA/11.17/FH96[G] 2017-03-18 Buccal Swab USA Washington G up_to_date 36.91 0.763
MuVs/Washington.USA/12.17/FH97[G] 2017-03-23 Buccal Swab USA Washington G up_to_date 35.13 0.63
MuVs/Washington.USA/14.17/FH98[G] 2017-04-06 Buccal Swab USA Washington G not_up_to_date 29.59 0.761
MuVs/Wisconsin.USA/41.06/FH99[G] 2006-10 unknown USA Wisconsin G unknown unknown 0.767
MuVs/Washington.USA/19.17/FH100[G] 2017-05-11 Buccal Swab USA Washington G up_to_date 29.44 0.782
MuVs/Missouri.USA/28.17/FH101[G] 2017-07 unknown USA Missouri G unknown unknown 0.797
MuVs/Ohio.USA/2.18/FH102[G] 2018-01 unknown USA Ohio G unknown unknown 0.762
MuVs/Washington.USA/4.17/FH103[G] 2017-01-29 Buccal Swab USA Washington G up_to_date 34.19 0.558
MuVs/Washington.USA/5.17/FH104[G] 2017-02-08 Buccal Swab USA Washington G up_to_date 31.96 0.744
MuVs/Washington.USA/6.17/FH105[G] 2017-02-10 Buccal Swab USA Washington G up_to_date 36.53 0.653
MuVs/Washington.USA/7.17/FH106[G] 2017-02-14 Buccal Swab USA Washington G not_up_to_date 27.98 0.671
MuVs/Wisconsin.USA/7.07/FH107[G] 2007-02 unknown USA Wisconsin G unknown unknown 0.8
MuVs/Wisconsin.USA/11.07/FH108[G] 2007-03 unknown USA Wisconsin G unknown unknown 0.939
MuVs/Wisconsin.USA/11.07/FH109[G] 2007-03 unknown USA Wisconsin G unknown unknown 0.939
MuVs/Wisconsin.USA/16.14/FH110[G] 2014-04 unknown USA Wisconsin G unknown unknown 0.919
MuVs/Wisconsin.USA/20.14/FH111[G] 2014-05 unknown USA Wisconsin G unknown unknown 0.94
MuVs/Wisconsin.USA/24.14/FH112[G] 2014-06 unknown USA Wisconsin G unknown unknown 0.873
MuVs/Wisconsin.USA/29.14/FH113[G] 2014-07 unknown USA Wisconsin G unknown unknown 0.925
MuVs/Missouri.USA/29.15/FH114[G] 2015-07 unknown USA Missouri G unknown unknown 0.841
MuVs/Wisconsin.USA/42.15/FH115[G] 2015-10 unknown USA Wisconsin G unknown unknown 0.868
MuVs/Wisconsin.USA/42.15/FH116[G] 2015-10 unknown USA Wisconsin G unknown unknown 0.881
MuVs/Wisconsin.USA/46.15/FH117[G] 2015-11 unknown USA Wisconsin G unknown unknown 0.841
MuVs/Wisconsin.USA/2.16/FH118[G] 2016-01 unknown USA Wisconsin G unknown unknown 0.906
MuVs/Ohio.USA/19.16/FH119[G] 2016-05 unknown USA Ohio G unknown unknown 0.926
MuVs/Wisconsin.USA/24.16/FH120[G] 2016-06 unknown USA Wisconsin G unknown unknown 0.885
MuVs/Wisconsin.USA/19.16/FH121[G] 2016-05 unknown USA Wisconsin G unknown unknown 0.931
MuVs/Missouri.USA/41.16/FH122[G] 2016-10 unknown USA Missouri G unknown unknown 0.855
MuVs/Missouri.USA/46.16/FH123[G] 2016-11 unknown USA Missouri G unknown unknown 0.876
MuVs/Missouri.USA/46.16/FH124[G] 2016-11 unknown USA Missouri G unknown unknown 0.903
MuVs/Missouri.USA/50.16/FH125[G] 2016-12 unknown USA Missouri G unknown unknown 0.878
MuVs/Wisconsin.USA/50.16/FH126[G] 2016-12 unknown USA Wisconsin G unknown unknown 0.876
MuVs/Missouri.USA/2.17/FH127[G] 2017-01 unknown USA Missouri G unknown unknown 0.827
MuVs/Ohio.USA/2.17/FH128[G] 2017-01 unknown USA Ohio G unknown unknown 0.901
MuVs/Missouri.USA/7.17/FH129[G] 2017-02 unknown USA Missouri G unknown unknown 0.835
MuVs/Ohio.USA/7.17/FH130[G] 2017-02 unknown USA Ohio G unknown unknown 0.887
MuVs/Wisconsin.USA/15.06/FH131[G] 2006-04 unknown USA Wisconsin G unknown unknown 0.81
MuVs/Ohio.USA/11.17/FH132[G] 2017-03 unknown USA Ohio G unknown unknown 0.862
MuVs/Missouri.USA/11.17/FH133[G] 2017-03 unknown USA Missouri G unknown unknown 0.855
MuVs/Missouri.USA/15.17/FH134[G] 2017-04 unknown USA Missouri G unknown unknown 0.847
MuVs/Missouri.USA/15.17/FH135[G] 2017-04 unknown USA Missouri G unknown unknown 0.863
MuVs/NorthCarolina.USA/11.17/FH136[G] 2017-03 unknown USA NorthCarolina G unknown unknown 0.841
MuVs/Wisconsin.USA/15.17/FH137[G] 2017-04 unknown USA Wisconsin G unknown unknown 0.855
MuVs/Missouri.USA/15.17/FH138[G] 2017-04 unknown USA Missouri G unknown unknown 0.821
MuVs/Alabama.USA/15.17/FH139[G] 2017-04 unknown USA Alabama G unknown unknown 0.834
MuVs/Missouri.USA/19.17/FH140[G] 2017-05 unknown USA Missouri G unknown unknown 0.835
MuVs/Wisconsin.USA/19.17/FH141[G] 2017-05 unknown USA Wisconsin G unknown unknown 0.847
MuVs/Washington.USA/8.17/FH142[G] 2017-02-22 Buccal Swab USA Washington G up_to_date 25.33 0.861
MuVs/Washington.USA/11.17/FH143[G] 2017-03-15 Buccal Swab USA Washington G up_to_date 28.34 0.867
MuVs/Washington.USA/12.17/FH144[G] 2017-03-27 Buccal Swab USA Washington G unknown 29.66 0.855
MuVs/Washington.USA/14.17/FH145[G] 2017-04-06 Buccal Swab USA Washington G up_to_date 21.45 0.909
MuVs/Washington.USA/15.17/FH146[G] 2017-04-18 Buccal Swab USA Washington G up_to_date 27.09 0.844
MuVs/Washington.USA/18.17/FH147[G] 2017-05-04 Buccal Swab USA Washington G up_to_date 28.86 0.882
MuVs/Washington.USA/20.17/FH148[G] 2017-05-24 Buccal Swab USA Washington G up_to_date 26.59 0.822
MuVs/Washington.USA/23.17/FH149[G] 2017-06-11 Buccal Swab USA Washington G unknown 33.05 0.843
MuVs/Washington.USA/23.17/FH150[G] 2017-06-12 Buccal Swab USA Washington G up_to_date 32.33 0.841
MuVs/Washington.USA/28.17/FH151[G] 2017-07-12 Buccal Swab USA Washington G up_to_date 24.18 0.877
MuVs/Washington.USA/16.17/FH152[G] 2017-04-17 Buccal Swab USA Washington G up_to_date 27.41 0.855
MuVs/Wisconsin.USA/41.06/FH153[G] 2006-10 unknown USA Wisconsin G unknown unknown 0.837
MuVs/Wisconsin.USA/7.07/FH154[G] 2007-02 unknown USA Wisconsin G unknown unknown 0.941
MuVs/Missouri.USA/33.17/FH155[G] 2017-08 unknown USA Missouri G unknown unknown 0.85
MuVs/Alabama.USA/50.17/FH156[G] 2017-12 unknown USA Alabama G unknown unknown 0.848
MuVs/Ohio.USA/46.17/FH157[G] 2017-11 unknown USA Ohio G unknown unknown 0.842
MuVs/Washington.USA/49.16/FH158[G] 2016-12-11 Buccal Swab USA Washington G unknown 30.55 0.842
MuVs/Wisconsin.USA/28.06/FH159[G] 2006-07 unknown USA Wisconsin G unknown unknown 0.842
MuVs/Washington.USA/1.17/FH160[G] 2017-01-03 Buccal Swab USA Washington G unknown 24.17 0.875
MuVs/Washington.USA/5.17/FH161[G] 2017-01-31 Buccal Swab USA Washington G up_to_date 23.05 0.916
MuVs/Washington.USA/5.17/FH162[G] 2017-02-02 Buccal Swab USA Washington G up_to_date 27.08 0.898
MuVs/Wisconsin.USA/51.15/FH163[G] 2015-12 unknown USA Wisconsin G unknown unknown 0.855
MuVs/Alabama.USA/7.17/FH164[G] 2017-02 unknown USA Alabama G unknown unknown 0.801
MuVs/Missouri.USA/24.17/FH165[G] 2017-06 unknown USA Missouri G unknown unknown 0.862
MuVs/Washington.USA/7.17/FH166[G] 2017-02-19 Buccal Swab USA Washington G up_to_date 27.96 0.851
