Anthony Underwood antunderwood

## gist:84197f895a5e9f16040ae6e5b8222810
The Tokyo Cascade is not the tallest building in Tokyo, but it's the tallest in its district, which is a densely-populated mixed neighborhood. Closer to the Cascade, one finds corporate offices, gated communities, and plush tourist attractions securely separated from the poorer residential buildings and low-cost coffin hotels further out. Standing far above the rooftops, the two towers of gleaming bronze, each eighty stories high, overshadow the busy Cascade Plaza. The Zen Garden Skybridge connects the two towers on the 71st floor (noting that in Japan the fourth floor is labeled fifth, so technically the skybridge is on the 70th). A massive holographic waterfall is projected as falling from the Skybridge using camouflaged emitters on the bridge and down the sides of the East and West Towers.

The buildings host several companies, all part of the same zaibatsu, and all on good terms with the Bureau of Onmyō, who has offices here (to secretly oversee their House of Zen). There are helipads on the top, and the

## weather.csv
"DATE","PRCP","TMAX","TMIN","RAIN"
"1948-01-01",0.47,51,42,"TRUE"
"1948-01-02",0.59,45,36,"TRUE"
"1948-01-03",0.42,45,35,"TRUE"
"1948-01-04",0.31,45,34,"TRUE"
"1948-01-05",0.17,45,32,"TRUE"
"1948-01-06",0.44,48,39,"TRUE"
"1948-01-07",0.41,50,40,"TRUE"
"1948-01-08",0.04,48,35,"TRUE"
"1948-01-09",0.12,50,31,"TRUE"

## dist_matrix.csv

          
            0
            1
            8
            9

            
              1
              0
              7
              8

            
              8
              7
              0
              1

            
              9
              8
              1
              0

## tree.nwk
(Wuhan/WH04/2020:0,((France/HDF-100002823145/2021:0,(France/HDF-100002521356/2021:0.000300973,(Germany/NW-RKI-I-088561/2021:0.000401298,Germany/NW-RKI-I-153620/2021:0.000167207,Germany/NW-RKI-I-088632/2021:0.000100324,Germany/NW-RKI-I-088607/2021:6.68829e-05,Germany/NW-RKI-I-069106/2021:0.00023409,(Germany/NW-RKI-I-153674/2021:0,(Germany/NW-RKI-I-088572/2021:6.68829e-05,Germany/NW-RKI-I-088616/2021:0.000133766,(Germany/NW-RKI-I-145025/2021:6.68829e-05,Germany/NW-RKI-I-144938/2021:0.000167207):6.68829e-05,Germany/NW-RKI-I-069031/2021:0.000100324,Germany/NW-RKI-I-145007/2021:0.000133766,Germany/NW-RKI-I-069084/2021:3.34415e-05,Germany/NW-RKI-I-144929/2021:6.68829e-05):3.34415e-05,(Germany/NW-RKI-I-088575/2021:0.000100324,Germany/NW-RKI-I-088568/2021:0.000100324):3.34415e-05,Germany/NW-RKI-I-088586/2021:0.000133766):3.34415e-05):0.000635387):6.6883e-05):6.68829e-05,((Denmark/DCGC-94791/2021:6.68829e-05,Denmark/DCGC-72175/2021:6.68829e-05):3.34415e-05,USA/IL-CDC-ASC210061804/2021:0.000133766):3.34415e-05,(India/T

## colours.csv

          
            id
            colour

            
              1127
              #696969

            
              8081
              #fd125b

            
              2/C/53/NMD7
              #0fc060

            
              209-36/84
              #a65651

            
              E701
              #c0135c

            
              E736
              #a65651

            
              ERL022789
              #ab2e94

            
              ERL023784
              #696969

            
              ERL032126
              #efe900

## graph.json
{
  "directed": true,
  "graph": {},
  "links": [
    {
      "coverage": 1.0,
      "identity": 0.997,
      "source": "card:ARO:3000005",
      "target": "ncbi:WP_063856692.1",
      "type": "RBH"

## variants_wide.csv

          
            Sample
            D614G
            N439K
            P323I
            A222V
            Y453F

            
              1
              D
              N
              P
              A
              F

            
              2
              D
              N
              P
              A
              F

            
              3
              D
              K
              I
              A
              Y

            
              4
              G
              N
              I
              V
              Y

            
              5
              G
              K
              P
              V
              F

## silvia_mock_data.csv

          
            Sample
            position
            nt

            
              Reference
              8782
              T

            
              Reference
              13066
              T

            
              Reference
              17858
              A

            
              Reference
              18060
              C

            
              Reference
              23403
              A

            
              ARG_1
              8782
              C

            
              ARG_1
              13066
              T

            
              ARG_1
              17858
              G

            
              ARG_1
              18060
              C

## variants.csv

          
            Sample
            variant
            allele

            
              1
              D614G
              D

            
              1
              N439K
              N

            
              1
              P323I
              P

            
              1
              A222V
              A

            
              1
              Y453F
              F

            
              2
              D614G
              D

            
              2
              N439K
              N

            
              2
              P323I
              P

            
              2
              A222V
              A

## MICs.tsv
ROW_IDX	COUNTRY_A	LABORATORY	ORIGIN	PATIENT_ID	LAST_NAME	FIRST_NAME	SEX	DATE_BIRTH	AGE	PAT_TYPE	WARD	INSTITUT	DEPARTMENT	WARD_TYPE	DATE_ADMIS	SPEC_NUM	SPEC_DATE	SPEC_TYPE	LOCAL_SPEC	SPEC_CODE	SPEC_REAS	ISOL_NUM	ORGANISM	LOCAL_ORG	ORG_TYPE	SEROTYPE	MRSA	VRE	BETA_LACT	ESBL	CARBAPENEM	MRSA_SCRN	INDUC_CLI	COMMENT	DATE_DATA	AMC_NM	AMK_NM	AMP_NM	ATM_NM	AZM_NM	CAZ_NM	CEP_NM	CFM_NM	CHL_NM	CIP_NM	CLI_NM	COL_NM	COP_NM	CRO_NM	CSL_NM	CTX_NM	CXA_NM	CXM_NM	CZO_NM	DAP_NM	DOR_NM	ENR_NM	ERY_NM	ETP_NM	FEP_NM	FOX_NM	GEN_NM	IPM_NM	LNZ_NM	LVX_NM	MAN_NM	MEM_NM	MFX_NM	MNO_NM	NAL_NM	NOR_NM	NTZ_NM	OFX_NM	OXA_NM	PEN_NM	PIP_NM	QDA_NM	RIF_NM	SAM_NM	SPT_NM	STR_NM	SXT_NM	TCC_NM	TCY_NM	TEC_NM	TGC_NM	TOB_NM	TZP_NM	VAN_NM
0.00000	COL	RET		G18000002												RB 141							eco	eco	-										2020-09-30		16				16				>2			<=0.5	>32							<=0.12			<=0.5	8	16	>8	<=0.25				<=0.25												>16							<=0.5		8
1.00000	COL	RET		G18000009												RB 149							kpn	kpn	-										2020-09-30		>32				2				>2			<=0.5	>32							>4			<=0.5	<=1	<=4	>8	8
	The Tokyo Cascade is not the tallest building in Tokyo, but it's the tallest in its district, which is a densely-populated mixed neighborhood. Closer to the Cascade, one finds corporate offices, gated communities, and plush tourist attractions securely separated from the poorer residential buildings and low-cost coffin hotels further out. Standing far above the rooftops, the two towers of gleaming bronze, each eighty stories high, overshadow the busy Cascade Plaza. The Zen Garden Skybridge connects the two towers on the 71st floor (noting that in Japan the fourth floor is labeled fifth, so technically the skybridge is on the 70th). A massive holographic waterfall is projected as falling from the Skybridge using camouflaged emitters on the bridge and down the sides of the East and West Towers.

	The buildings host several companies, all part of the same zaibatsu, and all on good terms with the Bureau of Onmyō, who has offices here (to secretly oversee their House of Zen). There are helipads on the top, and the
	"DATE","PRCP","TMAX","TMIN","RAIN"
	"1948-01-01",0.47,51,42,"TRUE"
	"1948-01-02",0.59,45,36,"TRUE"
	"1948-01-03",0.42,45,35,"TRUE"
	"1948-01-04",0.31,45,34,"TRUE"
	"1948-01-05",0.17,45,32,"TRUE"
	"1948-01-06",0.44,48,39,"TRUE"
	"1948-01-07",0.41,50,40,"TRUE"
	"1948-01-08",0.04,48,35,"TRUE"
	"1948-01-09",0.12,50,31,"TRUE"
	id	colour
	1127	#696969
	8081	#fd125b
	2/C/53/NMD7	#0fc060
	209-36/84	#a65651
	E701	#c0135c
	E736	#a65651
	ERL022789	#ab2e94
	ERL023784	#696969
	ERL032126	#efe900
	{
	"directed": true,
	"graph": {},
	"links": [
	{
	"coverage": 1.0,
	"identity": 0.997,
	"source": "card:ARO:3000005",
	"target": "ncbi:WP_063856692.1",
	"type": "RBH"
Sample	D614G	N439K	P323I	A222V	Y453F
1	D	N	P	A	F
2	D	N	P	A	F
3	D	K	I	A	Y
4	G	N	I	V	Y
5	G	K	P	V	F
Sample	position	nt
Reference	8782	T
Reference	13066	T
Reference	17858	A
Reference	18060	C
Reference	23403	A
ARG_1	8782	C
ARG_1	13066	T
ARG_1	17858	G
ARG_1	18060	C
Sample	variant	allele
1	D614G	D
1	N439K	N
1	P323I	P
1	A222V	A
1	Y453F	F
2	D614G	D
2	N439K	N
2	P323I	P
2	A222V	A
	ROW_IDX COUNTRY_A LABORATORY ORIGIN PATIENT_ID LAST_NAME FIRST_NAME SEX DATE_BIRTH AGE PAT_TYPE WARD INSTITUT DEPARTMENT WARD_TYPE DATE_ADMIS SPEC_NUM SPEC_DATE SPEC_TYPE LOCAL_SPEC SPEC_CODE SPEC_REAS ISOL_NUM ORGANISM LOCAL_ORG ORG_TYPE SEROTYPE MRSA VRE BETA_LACT ESBL CARBAPENEM MRSA_SCRN INDUC_CLI COMMENT DATE_DATA AMC_NM AMK_NM AMP_NM ATM_NM AZM_NM CAZ_NM CEP_NM CFM_NM CHL_NM CIP_NM CLI_NM COL_NM COP_NM CRO_NM CSL_NM CTX_NM CXA_NM CXM_NM CZO_NM DAP_NM DOR_NM ENR_NM ERY_NM ETP_NM FEP_NM FOX_NM GEN_NM IPM_NM LNZ_NM LVX_NM MAN_NM MEM_NM MFX_NM MNO_NM NAL_NM NOR_NM NTZ_NM OFX_NM OXA_NM PEN_NM PIP_NM QDA_NM RIF_NM SAM_NM SPT_NM STR_NM SXT_NM TCC_NM TCY_NM TEC_NM TGC_NM TOB_NM TZP_NM VAN_NM
	0.00000 COL RET G18000002 RB 141 eco eco - 2020-09-30 16 16 >2 <=0.5 >32 <=0.12 <=0.5 8 16 >8 <=0.25 <=0.25 >16 <=0.5 8
	1.00000 COL RET G18000009 RB 149 kpn kpn - 2020-09-30 >32 2 >2 <=0.5 >32 >4 <=0.5 <=1 <=4 >8 8