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Ae-aegypti-FL01M|KX838904|2016-08-22|usa.fasta.gz
Ae-aegypti-FL02M|KX838905|2016-08-23|usa.fasta.gz
Ae-aegypti-FL03M|KX838906|2016-08-23|usa.fasta.gz
Ae-aegypti-FL04M|KX922708|2016-09-04|usa.fasta.gz
Ae-aegypti-FL05M|KX922708|2016-09-09|usa.fasta.gz
Ae-aegypti-FL06M|XX|2016-09-20|usa.fasta.gz
Ae-aegypti-FL08M|XX|2016-10-05|usa.fasta.gz
FL001Sa|XX|2016-03-22|usa_ex_martinigue.fasta.gz
FL008U|XX|2016-06-15|usa_ex_puerto_rico.fasta.gz
FL010U|KX842449|2016-06-22|usa.fasta.gz
FL016U|XX|2016-07-03|usa_ex_puerto_rico.fasta.gz
FL021U|KX922703|2016-07-19|usa.fasta.gz
FL022U|XX|2016-07-16|usa.fasta.gz
FL030U|KX922704|2016-08-02|usa.fasta.gz
FL032U|KX922705|2016-08-05|usa.fasta.gz
FL036SE|XX|2016-08-02|usa.fasta.gz
FL038U|KX922706|2016-08-05|usa.fasta.gz
FL039U|KX922707|2016-08-17|usa.fasta.gz
FL046Se|XX|2017-07-26|Cuba.fasta
FL047U|XX|2017-08-08|Cuba.fasta
FL049U|XX|2017-09-24|Cuba.fasta
FL051Se|XX|2017-07-17|Cuba.fasta
FL052U|XX|2017-08-05|Cuba.fasta
FL055Se|XX|2017-08-13|Cuba.fasta
FL057U|XX|2017-07-17|Cuba.fasta
Hu0015Sa|KX832731|2016-08-22|usa.fasta.gz
Hu0046SA|XX|2017-04-19|usa_ex_cuba.fasta.gz
README.md
ZC188Se|XX|2016-01-16|colombia.fasta.gz
ZC192Se|XX|2016-01-07|colombia.fasta.gz
ZC199Se|XX|2016-01-10|colombia.fasta.gz
ZC204Se|XX|2016-01-05|colombia.fasta.gz
ZC207Se|XX|2016-01-09|colombia.fasta.gz

README.md

Sequence MetaData

Scripps ID Patient ID Sample type Quality score % Coverage Average Depth Onset Collection Days post onset Local or travel Location of infection GE/ul RNA GE/mL sample Sequencing status Consensus name Merged Bam File
FL001Sa 001 Saliva *** 99.71 46616.27 2016.03.18 2016.03.22 4 Travel Martinique 11 3.3E+03 coding-complete ZF1_01Sa_XX_2016-03-22 usa_ex_martinique ZF1.c1.Sa.a1.l1.l3.l4.r1
FL008U 008 Urine *** 90.07 35012.49 2016.06.15 2016.06.21 6 Travel Puerto Rico 4 1.1E+03 coding-complete ZF8_08U_XX_2016-06-21 usa_ex_puerto_rico ZF8.c1.UR.a1.l1.l2.r1
FL010U 010 Urine **** 97.69 55330.48 2016.06.17 2016.06.22 5 Local? USA: Florida 213 6.1E+04 coding-complete ZF10_10U_KX842499 2016-06-22 usa_ex_USA ZF10.c1.UR.a1.l1.r1
FL016U 016 Urine *** 99.88 75158.72 2016.06.28 2016.07.03 5 Travel Puerto Rico 14 4.0E+03 coding-complete ZF16_16U_XX_2016-07-03 usa_ex_puerto_rico ZF16.c1.UR.a1.l1.l2.l3.l4.l5.r1
FL021U 021 Urine *** 97.45 52361.36 2016.07.09 2016.07.19 10 Local USA: Florida 50 1.4E+04 coding-complete ZF21_21U_XX_2016-07-19 usa ZF21.c1.UR.a1.l1.l2.l3.r1
FL022U 022 Urine *** 97.77 51135.60 2016.07.16 2016.07.16 6 Local USA: Florida 11 3.0E+03 coding-complete ZF22_22U_XX_2016-07-16 usa ZF22.c1.UR.a1.l1.l2.l3.l4.r1
FL030U 030 Urine *** 99.75 57779.63 2016.07.31 2016.08.02 2 Local USA: Florida 36 1.0E+04 coding-complete ZF30_30U_XX_2016-08-02 usa ZF30.c1.UR.a1.l1.l2.l3.r1
FL032U 032 Urine *** 99.75 51483.94 2016.07.29 2016.08.05 7 Local USA: Florida 75 2.1E+04 coding-complete ZF32_32U_XX_2016-08-05 usa ZF32.c1.UR.a1.l1.l2.l3.r1
FL036Se 036 Serum *** 99.73 101435.66 2016.08.02 2016.08.04 2 Local USA: Florida 11 3.2E+03 coding-complete FL036SE_XX_2016-08-02_usa ZF36.c1.SR.a1.l1.l2.l3.l4.l5.l6.l7.r1.l5.l6.r2
FL038U 038 Urine *** 99.76 81750.77 2016.08.04 2016.08.05 1 Local USA: Florida 38 1.1E+04 coding-complete ZF38_38U_XX_2016-08-05 usa ZF38.c1.UR.a1.l1.l2.l3.l4.r1
FL039U 039 Urine **** 99.75 70253.99 2016.08.12 2016.08.17 5 Local USA: Florida 1276 3.6E+05 coding-complete ZF39_39U_XX_2016-08-17 usa ZF39.c1.UR.a1.l1.l2.l3.r1
Hu0015Sa Hu0015 Saliva *** 99.75 89934.25 2016.08.19 2016.08.24 5 Local USA: Florida 38 21610.23 coding-complete ZL2_Hu0015_KX832731 2016-08-22 usa ZL2.c1.SA.a1.l1.l2.r1
FL01M 7501 Mosquito **** 99.75 141038.31 2016.08.22 Local USA: Florida 4563 9.1E+06 coding-complete Ae-aegypti_ZM1_7501_KX838904_2016-08-22_usa ZM1.c1.MO.a1.l1.l2.r1
FL02M 7719 Mosquito **** 99.74 137263.85 2016.08.23 Local USA: Florida 279 5.6E+05 coding-complete Ae-aegypti_ZM2_7719_KX838905_2016-08-23_usa ZM2.c1.MO.a1.l1.l2.r1
FL03M 7727 Mosquito **** 99.83 139787.57 2016.08.23 Local USA: Florida 22549 4.5E+07 coding-complete Ae-aegypti_ZM3_7727_KX838906_2016-08-23_usa ZM3.c1.MO.a1.l1.l2.r1
FL04M 16-10416 Mosquito **** 99.72 45505.39 2016.09.04 Local USA: Florida 102 4.4E+04 coding-complete Ae-aegypti_ZM4_16-10416_XX_2016-09-04_usa ZM4.c1.MO.a1.l1.l2.r1
FL05M 16-3125 Mosquito **** 99.74 52530.58 2016.09.09 Local USA: Florida 447 1.9E+05 coding-complete Ae-aegypti_ZM5_16-3125_XX_2016-09-09_usa ZM5.c1.MO.a1.l1.l2.r1
FL06M Mosquito **** 99.71 25181.33 2016.09.20 Local USA: Florida coding-complete FL06M_XX_2016-09-20_usa ZM6.c1.MO.a1.l1.l2.r1
FL08M pool#8 Mosquito **** 97.70 68629.61 2016.10.05 Local USA: Florida 61 2.6E+04 coding-complete FL08M_XX_2016-10-05_usa ZM8.c1.MO.a1.l1.l2.r1
ZC188Se 423568715 Serum **** 98.26 29394.90 2016.01.16 Colombia 36 1.5E+04 coding-complete ZC188_423568715_XX_2016-01-16_colombia ZC188.c1.SR.a1.l3.l4.r1
ZC192Se 423401315 Serum **** 98.36 30396.29 2016.01.07 Colombia 39 1.7E+04 coding-complete ZC192_423401315_XX_2016-01-07_colombia ZC192.c1.SR.a1.l3.l4.r1
ZC204Se 424439915 Serum **** 99.74 29003.25 2016.01.06 Colombia 48 2.1E+04 coding-complete ZC204_424439915_XX_2016-01-05_colombia ZC204.c1.SR.a1.l1.l2.r1
ZC207Se 423217515 Serum **** 96.68 19477.70 2016.01.09 Colombia 16 6.7E+04 coding-complete ZC207_423217515_XX_2016-01-09_colombia ZC207.c1.SR.a1.l1.l2.r1
ZC199Se 4238001315 Serum *** 97.44 98358.93 2016.01.10 Colombia 10 4.3E+03 coding-complete ZC199Se_XX_2016-01-10_colombia ZC199.c1.SR.a1.l1.l2.l3.l4.l5.l6.l7.r1
Hu0046Sa Hu0046 Saliva **** 98.20 10498 2017.04.18 2017.04.19 1 travel Cuba 16 63830 coding-complete Hu0046SA_XX_2017-04-19_usa_ex_cuba.fasta ZT1.c1.SA.a1.l1.l2.r1

Quality

**** Complete coding sequence, no apparent contamination in aligned bam file
***	Complete coding sequence, some contamination in aligned bam file (confident in consensus)
**	Partial coding sequence, no apparent contamination in aligned bam file
*	Partial coding sequence, some contamination in aligned bam file