-
Notifications
You must be signed in to change notification settings - Fork 2
Files
/
Copy pathexample_annotatedAMRreport.tsv
Latest commit
41 lines (41 loc) · 11.8 KB
/
example_annotatedAMRreport.tsv
1 | Name | Protein identifier | Contig id | Start | Stop | Strand | Gene symbol | Sequence name | Species interpretation | Context | Org interpretation | Drug | Scope | Element type | Element subtype | Class | Subclass | Method | Target length | Reference sequence length | % Coverage of reference sequence | % Identity to reference sequence | Alignment length | Accession of closest sequence | Name of closest sequence | HMM id | HMM description |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2 | ERR257656 | NA | UNYN01000002.1 | 474533 | 477682 | - | oqxB19 | multidrug efflux RND transporter permease subunit OqxB19 | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | ALLELEX | 1050 | 1050 | 100.00 | 100.00 | 1050 | WP_004149399.1 | multidrug efflux RND transporter permease subunit OqxB19 | NA | NA |
3 | ERR257656 | NA | UNYN01000002.1 | 477709 | 478881 | - | oqxA3 | multidrug efflux RND transporter periplasmic adaptor subunit OqxA3 | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | ALLELEX | 391 | 391 | 100.00 | 100.00 | 391 | WP_004890321.1 | multidrug efflux RND transporter periplasmic adaptor subunit OqxA3 | NA | NA |
4 | ERR257656 | NA | UNYN01000003.1 | 557748 | 558605 | - | blaSHV-33 | broad-spectrum class A beta-lactamase SHV-33 | Klebsiella pneumoniae; v1.1 | core | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_023325206.1 | broad-spectrum class A beta-lactamase SHV-33 | NA | NA |
5 | ERR257656 | NA | UNYN01000006.1 | 15444 | 15860 | + | fosA | FosA5 family fosfomycin resistance glutathione transferase | Klebsiella pneumoniae; v1.1 | core | wt (S) | fosfomycin | core | AMR | AMR | FOSFOMYCIN | FOSFOMYCIN | EXACTX | 139 | 139 | 100.00 | 100.00 | 139 | WP_004146118.1 | FosA5 family fosfomycin resistance glutathione transferase | NA | NA |
6 | ERR257656 | NA | UNYN01000008.1 | 196592 | 197773 | + | emrD | multidrug efflux MFS transporter EmrD | Klebsiella pneumoniae; v1.1 | plus | AMR | AMR | EFFLUX | EFFLUX | BLASTX | 394 | 394 | 100.00 | 99.24 | 394 | ACN65732.1 | multidrug efflux MFS transporter EmrD | NA | NA | |||
7 | ERR257656 | NA | UNYN01000015.1 | 25521 | 26378 | - | blaTEM-1 | broad-spectrum class A beta-lactamase TEM-1 | Klebsiella pneumoniae; v1.1 | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_000027057.1 | broad-spectrum class A beta-lactamase TEM-1 | NA | NA | |
8 | ERR257656 | NA | UNYN01000019.1 | 3447 | 3917 | + | dfrA1 | trimethoprim-resistant dihydrofolate reductase DfrA1 | Klebsiella pneumoniae; v1.1 | trimethoprim | core | AMR | AMR | TRIMETHOPRIM | TRIMETHOPRIM | EXACTX | 157 | 157 | 100.00 | 100.00 | 157 | WP_071846295.1 | trimethoprim-resistant dihydrofolate reductase DfrA1 | NA | NA | ||
9 | ERR257656 | NA | UNYN01000019.1 | 4612 | 5400 | + | aadA22 | ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA22 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | AMINOGLYCOSIDE | STREPTOMYCIN | BLASTX | 263 | 263 | 100.00 | 93.54 | 263 | WP_071846321.1 | ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA22 | NA | NA | |||
10 | ERR257656 | NA | UNYN01000019.1 | 5908 | 6744 | + | sul1 | sulfonamide-resistant dihydropteroate synthase Sul1 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | SULFONAMIDE | SULFONAMIDE | EXACTX | 279 | 279 | 100.00 | 100.00 | 279 | WP_000259031.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | NA | NA | |||
11 | EuSCAPE_DE047 | NA | NZ_UKKZ01000001.1 | 122816 | 123673 | - | blaSHV-28 | broad-spectrum class A beta-lactamase SHV-28 | Klebsiella pneumoniae; v1.1 | core | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_004179754.1 | broad-spectrum class A beta-lactamase SHV-28 | NA | NA |
12 | EuSCAPE_DE047 | NA | NZ_UKKZ01000003.1 | 205730 | 208360 | - | gyrA_S83Y | Klebsiella pneumoniae quinolone resistant GyrA | Klebsiella pneumoniae; v1.1 | ciprofloxacin | core | AMR | POINT | QUINOLONE | QUINOLONE | POINTX | 877 | 877 | 100.00 | 99.77 | 877 | WP_117036963.1 | DNA gyrase subunit A GyrA | NA | NA | ||
13 | EuSCAPE_DE047 | NA | NZ_UKKZ01000022.1 | 70069 | 70485 | - | fosA | FosA5 family fosfomycin resistance glutathione transferase | Klebsiella pneumoniae; v1.1 | core | wt (S) | fosfomycin | core | AMR | AMR | FOSFOMYCIN | FOSFOMYCIN | EXACTX | 139 | 139 | 100.00 | 100.00 | 139 | WP_004146118.1 | FosA5 family fosfomycin resistance glutathione transferase | NA | NA |
14 | EuSCAPE_DE047 | NA | NZ_UKKZ01000042.1 | 1745 | 2215 | + | dfrA14 | trimethoprim-resistant dihydrofolate reductase DfrA14 | Klebsiella pneumoniae; v1.1 | trimethoprim | core | AMR | AMR | TRIMETHOPRIM | TRIMETHOPRIM | EXACTX | 157 | 157 | 100.00 | 100.00 | 157 | WP_004201280.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | NA | NA | ||
15 | EuSCAPE_DE047 | NA | NZ_UKKZ01000049.1 | 533 | 1174 | - | qnrB1 | quinolone resistance pentapeptide repeat protein QnrB1 | Klebsiella pneumoniae; v1.1 | ciprofloxacin | core | AMR | AMR | QUINOLONE | QUINOLONE | ALLELEX | 214 | 214 | 100.00 | 100.00 | 214 | WP_014386481.1 | quinolone resistance pentapeptide repeat protein QnrB1 | NA | NA | ||
16 | EuSCAPE_DE047 | NA | NZ_UKKZ01000053.1 | 697 | 1569 | + | blaCTX-M-15 | extended-spectrum class A beta-lactamase CTX-M-15 | Klebsiella pneumoniae; v1.1 | ceftriaxone | core | AMR | AMR | BETA-LACTAM | CEPHALOSPORIN | ALLELEX | 291 | 291 | 100.00 | 100.00 | 291 | WP_000239590.1 | extended-spectrum class A beta-lactamase CTX-M-15 | NA | NA | ||
17 | EuSCAPE_DE047 | NA | NZ_UKKZ01000054.1 | 1738 | 2919 | - | tet(D) | tetracycline efflux MFS transporter Tet(D) | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | TETRACYCLINE | TETRACYCLINE | EXACTX | 394 | 394 | 100.00 | 100.00 | 394 | WP_001039466.1 | tetracycline efflux MFS transporter Tet(D) | NA | NA | |||
18 | EuSCAPE_HR089 | NA | NZ_UJHW01000003.1 | 398499 | 401648 | - | oqxB | multidrug efflux RND transporter permease subunit OqxB | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | BLASTX | 1050 | 1050 | 100.00 | 99.90 | 1050 | WP_016947602.1 | multidrug efflux RND transporter permease subunit OqxB25 | NA | NA |
19 | EuSCAPE_HR089 | NA | NZ_UJHW01000003.1 | 401675 | 402847 | - | oqxA | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | EXACTX | 391 | 391 | 100.00 | 100.00 | 391 | WP_002914189.1 | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | NA | NA |
20 | EuSCAPE_HR089 | NA | NZ_UJHW01000004.1 | 56137 | 58767 | - | gyrA_S83I | Klebsiella pneumoniae quinolone resistant GyrA | Klebsiella pneumoniae; v1.1 | ciprofloxacin | core | AMR | POINT | QUINOLONE | QUINOLONE | POINTX | 877 | 877 | 100.00 | 99.66 | 877 | WP_117036963.1 | DNA gyrase subunit A GyrA | NA | NA | ||
21 | EuSCAPE_HR089 | NA | NZ_UJHW01000007.1 | 251361 | 251774 | - | fosA | FosA5 family fosfomycin resistance glutathione transferase | Klebsiella pneumoniae; v1.1 | core | wt (S) | fosfomycin | core | AMR | AMR | FOSFOMYCIN | FOSFOMYCIN | BLASTX | 138 | 139 | 99.28 | 99.28 | 138 | WP_004146118.1 | FosA5 family fosfomycin resistance glutathione transferase | NA | NA |
22 | EuSCAPE_HR089 | NA | NZ_UJHW01000034.1 | 5328 | 6116 | + | aadA1 | ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | AMINOGLYCOSIDE | STREPTOMYCIN | EXACTX | 263 | 263 | 100.00 | 100.00 | 263 | WP_001206316.1 | ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 | NA | NA | |||
23 | EuSCAPE_HR089 | NA | NZ_UJHW01000034.1 | 6624 | 7460 | + | sul1 | sulfonamide-resistant dihydropteroate synthase Sul1 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | SULFONAMIDE | SULFONAMIDE | EXACTX | 279 | 279 | 100.00 | 100.00 | 279 | WP_000259031.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | NA | NA | |||
24 | EuSCAPE_HR089 | NA | NZ_UJHW01000039.1 | 2643 | 3500 | + | blaSHV-1 | broad-spectrum class A beta-lactamase SHV-1 | Klebsiella pneumoniae; v1.1 | core | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_001620095.1 | broad-spectrum class A beta-lactamase SHV-1 | NA | NA |
25 | EuSCAPE_HR089 | NA | NZ_UJHW01000040.1 | 1738 | 2919 | - | tet(D) | tetracycline efflux MFS transporter Tet(D) | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | TETRACYCLINE | TETRACYCLINE | EXACTX | 394 | 394 | 100.00 | 100.00 | 394 | WP_001039466.1 | tetracycline efflux MFS transporter Tet(D) | NA | NA | |||
26 | INF014 | NA | NZ_CP031810.1 | 1468787 | 1469644 | + | blaSHV-11 | broad-spectrum class A beta-lactamase SHV-11 | Klebsiella pneumoniae; v1.1 | core | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_004176269.1 | broad-spectrum class A beta-lactamase SHV-11 | NA | NA |
27 | INF014 | NA | NZ_CP031810.1 | 3312262 | 3312678 | - | fosA | FosA5 family fosfomycin resistance glutathione transferase | Klebsiella pneumoniae; v1.1 | core | wt (S) | fosfomycin | core | AMR | AMR | FOSFOMYCIN | FOSFOMYCIN | BLASTX | 139 | 139 | 100.00 | 98.56 | 139 | WP_004146118.1 | FosA5 family fosfomycin resistance glutathione transferase | NA | NA |
28 | INF014 | NA | NZ_CP031810.1 | 4053958 | 4055139 | - | emrD | multidrug efflux MFS transporter EmrD | Klebsiella pneumoniae; v1.1 | plus | AMR | AMR | EFFLUX | EFFLUX | BLASTX | 394 | 394 | 100.00 | 99.49 | 394 | ACN65732.1 | multidrug efflux MFS transporter EmrD | NA | NA | |||
29 | INF014 | NA | NZ_CP031810.1 | 5193693 | 5196842 | - | oqxB19 | multidrug efflux RND transporter permease subunit OqxB19 | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | ALLELEX | 1050 | 1050 | 100.00 | 100.00 | 1050 | WP_004149399.1 | multidrug efflux RND transporter permease subunit OqxB19 | NA | NA |
30 | INF014 | NA | NZ_CP031810.1 | 5196869 | 5198041 | - | oqxA | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | EXACTX | 391 | 391 | 100.00 | 100.00 | 391 | WP_002914189.1 | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | NA | NA |
31 | INF014 | NA | NZ_CP031811.1 | 39972 | 40829 | + | blaTEM-1 | broad-spectrum class A beta-lactamase TEM-1 | Klebsiella pneumoniae; v1.1 | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_000027057.1 | broad-spectrum class A beta-lactamase TEM-1 | NA | NA | |
32 | INF014 | NA | NZ_CP031811.1 | 41556 | 42389 | - | aph(6)-Id | aminoglycoside O-phosphotransferase APH(6)-Id | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | AMINOGLYCOSIDE | STREPTOMYCIN | EXACTX | 278 | 278 | 100.00 | 100.00 | 278 | WP_000480968.1 | aminoglycoside O-phosphotransferase APH(6)-Id | NA | NA | |||
33 | INF014 | NA | NZ_CP031811.1 | 42392 | 43192 | - | aph(3'')-Ib | aminoglycoside O-phosphotransferase APH(3'')-Ib | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | AMINOGLYCOSIDE | STREPTOMYCIN | EXACTX | 267 | 267 | 100.00 | 100.00 | 267 | WP_001082319.1 | aminoglycoside O-phosphotransferase APH(3'')-Ib | NA | NA | |||
34 | INF014 | NA | NZ_CP031811.1 | 43256 | 44068 | - | sul2 | sulfonamide-resistant dihydropteroate synthase Sul2 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | SULFONAMIDE | SULFONAMIDE | EXACTX | 271 | 271 | 100.00 | 100.00 | 271 | WP_001043260.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | NA | NA | |||
35 | INF014 | NA | NZ_CP031811.1 | 54937 | 55785 | + | sul1 | sulfonamide-resistant dihydropteroate synthase Sul1 | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | SULFONAMIDE | SULFONAMIDE | EXACTX | 283 | 283 | 100.00 | 100.00 | 283 | WP_000946487.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | NA | NA | |||
36 | INF014 | NA | NZ_CP031811.1 | 56133 | 56945 | + | aph(3')-Ia | aminoglycoside O-phosphotransferase APH(3')-Ia | Klebsiella pneumoniae; v1.1 | core | AMR | AMR | AMINOGLYCOSIDE | KANAMYCIN | EXACTX | 271 | 271 | 100.00 | 100.00 | 271 | WP_000018330.1 | aminoglycoside O-phosphotransferase APH(3')-Ia | NA | NA | |||
37 | INF014 | NA | NZ_CP031811.1 | 60309 | 60779 | + | dfrA14 | trimethoprim-resistant dihydrofolate reductase DfrA14 | Klebsiella pneumoniae; v1.1 | trimethoprim | core | AMR | AMR | TRIMETHOPRIM | TRIMETHOPRIM | EXACTX | 157 | 157 | 100.00 | 100.00 | 157 | WP_004201280.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | NA | NA | ||
38 | SGH10 | NA | CP025080.1 | 1174414 | 1177563 | - | oqxB19 | multidrug efflux RND transporter permease subunit OqxB19 | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | ALLELEX | 1050 | 1050 | 100.00 | 100.00 | 1050 | WP_004149399.1 | multidrug efflux RND transporter permease subunit OqxB19 | NA | NA |
39 | SGH10 | NA | CP025080.1 | 1177590 | 1178762 | - | oqxA | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | Klebsiella pneumoniae; v1.1 | core | wt (S) | multiple drug | core | AMR | AMR | PHENICOL/QUINOLONE | PHENICOL/QUINOLONE | EXACTX | 391 | 391 | 100.00 | 100.00 | 391 | WP_002914189.1 | multidrug efflux RND transporter periplasmic adaptor subunit OqxA | NA | NA |
40 | SGH10 | NA | CP025080.1 | 2859578 | 2860435 | + | blaSHV-11 | broad-spectrum class A beta-lactamase SHV-11 | Klebsiella pneumoniae; v1.1 | core | wt (R) | ampicillin | core | AMR | AMR | BETA-LACTAM | BETA-LACTAM | ALLELEX | 286 | 286 | 100.00 | 100.00 | 286 | WP_004176269.1 | broad-spectrum class A beta-lactamase SHV-11 | NA | NA |
41 | SGH10 | NA | CP025080.1 | 4733497 | 4733913 | - | fosA | FosA5 family fosfomycin resistance glutathione transferase | Klebsiella pneumoniae; v1.1 | core | wt (S) | fosfomycin | core | AMR | AMR | FOSFOMYCIN | FOSFOMYCIN | EXACTX | 139 | 139 | 100.00 | 100.00 | 139 | WP_004146118.1 | FosA5 family fosfomycin resistance glutathione transferase | NA | NA |