TB-Profiler result

Run: ERR4820112
Summary

Run ID: ERR4820112

Sample name:

Date: 2024-10-04T05:25:53.289640

Number of reads: 3620434

Percentage reads mapped: 91.04

Median coverage: 73.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.1.1 Euro-American (X-type) RD183 0.92
lineage4 Euro-American None 0.98
lineage4.1.1 Euro-American (X-type) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8156 c.855T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8288 c.987T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8294 c.993T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8315 c.1014G>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8318 c.1017C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8324 c.1023T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8619 c.1318T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8627 c.1326C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8633 c.1332C>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8645 c.1344C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8655 p.Ile452Val missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 8666 c.1365G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8693 c.1392T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8694 c.1393C>T synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575824 c.477T>C synonymous_variant 0.13 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
nusG 734421 c.168A>G synonymous_variant 0.14 rifampicin
nusG 734424 c.171G>T synonymous_variant 0.13 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.15 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>T synonymous_variant 0.17 rifampicin
rpoB 760130 p.Asp108Glu missense_variant 0.14 rifampicin Uncertain significance
rpoB 760142 c.336C>G synonymous_variant 0.13 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760971 c.1165C>A synonymous_variant 0.14 rifampicin
rpoB 760994 c.1188G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761201 c.1395G>A synonymous_variant 0.13 rifampicin
rpoB 761204 c.1398C>G synonymous_variant 0.14 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.14 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761492 c.1686G>C synonymous_variant 0.15 rifampicin
rpoB 762134 c.2328C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762510 p.Ala902Pro missense_variant 0.12 rifampicin Uncertain significance
rpoC 764575 c.1206T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 766528 c.3159T>C synonymous_variant 0.15 rifampicin
rpoC 766534 c.3165C>G synonymous_variant 0.16 rifampicin
rpoC 766537 c.3168G>A synonymous_variant 0.17 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.19 rifampicin
rpoC 766549 c.3180G>T synonymous_variant 0.17 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.12 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.14 rifampicin
rpoC 766792 c.3423C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766795 c.3426C>T synonymous_variant 0.15 rifampicin
rpoC 766801 c.3432C>T synonymous_variant 0.14 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.96 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.94 linezolid
rplC 801312 c.504G>C synonymous_variant 0.12 linezolid
rplC 801348 c.540T>G synonymous_variant 0.13 linezolid
rplC 801357 c.549T>C synonymous_variant 0.12 linezolid
fbiC 1303551 c.621G>C synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fbiC 1303578 c.648G>A synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fbiC 1303584 c.654C>A synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fbiC 1303590 c.660A>G synonymous_variant 0.12 pretomanid
delamanid
clofazimine
fbiC 1303611 c.681G>C synonymous_variant 0.12 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834336 c.795C>G synonymous_variant 0.17 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.12 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2715658 c.-326C>G upstream_gene_variant 1.0 kanamycin
amikacin
ahpC 2726210 c.18T>C synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv2477c 2783956 c.87T>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859457 p.Val321Ala missense_variant 0.26 bedaquiline
clofazimine
pepQ 2859528 c.891T>C synonymous_variant 0.12 bedaquiline
clofazimine
Rv2752c 3064566 c.1626G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064590 c.1602C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3064596 c.1596G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064599 c.1593A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3064602 c.1590T>G synonymous_variant 0.14 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448491 c.-13C>T upstream_gene_variant 1.0 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625729 c.885A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625747 c.-837G>T upstream_gene_variant 0.12 rifampicin
bedaquiline
mtrB 3625755 p.Ala287Thr missense_variant 0.13 rifampicin Uncertain significance
bedaquiline
fbiA 3641447 p.Thr302Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
rpoA 3877553 p.Glu319Lys missense_variant 0.94 rifampicin Not assoc w R
rpoA 3878742 c.-235G>A upstream_gene_variant 0.17 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.13 rifampicin
rpoA 3879004 c.-499_-497delAAGinsCGA upstream_gene_variant 0.13 rifampicin
rpoA 3879016 c.-509A>G upstream_gene_variant 0.17 rifampicin
rpoA 3879022 c.-515G>C upstream_gene_variant 0.17 rifampicin
rpoA 3879043 c.-536C>G upstream_gene_variant 0.17 rifampicin
clpC1 4038508 c.2197C>T synonymous_variant 0.14 pyrazinamide
clpC1 4038519 p.Arg729Gln missense_variant 0.13 pyrazinamide
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.98 ethambutol Not assoc w R
embA 4244856 p.Ala542Pro missense_variant 0.17 ethambutol
embA 4244885 c.1653A>G synonymous_variant 0.18 ethambutol
embA 4244897 c.1665T>G synonymous_variant 0.15 ethambutol
embA 4244903 c.1671G>C synonymous_variant 0.15 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.13 ethambutol
embB 4248457 c.1944T>C synonymous_variant 0.13 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.97 ethambutol Not assoc w R
whiB6 4338498 p.Glu8Asp missense_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin