TB-Profiler result

Run: ERR11466072
Summary

Run ID: ERR11466072

Sample name:

Date: 2024-10-05T01:17:42.621759

Number of reads: 4617681

Percentage reads mapped: 99.4

Median coverage: 110.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.98
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.92
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
gyrB 6140 p.Val301Leu missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7532 c.231T>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7865 c.564T>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 8784 p.Arg495Cys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9267 p.Asn656Gly missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 9275 c.1974G>A synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575772 p.Val142Ala missense_variant 0.11 isoniazid
ethionamide
mshA 575782 c.435G>C synonymous_variant 0.11 isoniazid
ethionamide
mshA 575785 c.438T>C synonymous_variant 0.11 isoniazid
ethionamide
mshA 575795 p.Ile150Val missense_variant 0.12 isoniazid
ethionamide
mshA 575800 c.453G>C synonymous_variant 0.13 isoniazid
ethionamide
mshA 575803 c.456C>T synonymous_variant 0.15 isoniazid Not assoc w R - Interim
ethionamide
mshA 575821 c.474G>C synonymous_variant 0.24 isoniazid
ethionamide
mshA 575842 c.495G>C synonymous_variant 0.22 isoniazid
ethionamide
mshA 575864 c.517T>C synonymous_variant 0.16 isoniazid
ethionamide
mshA 575869 c.522G>A synonymous_variant 0.22 isoniazid
ethionamide
ccsA 620649 c.759A>G synonymous_variant 0.12 kanamycin
capreomycin
amikacin
ccsA 620652 c.762C>G synonymous_variant 0.11 kanamycin
capreomycin
amikacin
nusG 734499 c.246G>C synonymous_variant 0.19 rifampicin
nusG 734541 c.288A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760136 c.330G>A synonymous_variant 0.15 rifampicin
rpoB 760139 c.333A>T synonymous_variant 0.15 rifampicin
rpoB 760142 c.336C>G synonymous_variant 0.16 rifampicin
rpoB 760178 c.372G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760181 c.375T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.12 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760457 c.651C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>T synonymous_variant 0.13 rifampicin
rpoB 761288 c.1482G>T synonymous_variant 0.16 rifampicin
rpoB 761645 c.1839C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.14 rifampicin
rpoB 761666 c.1860G>C synonymous_variant 0.13 rifampicin
rpoB 761669 c.1863C>T synonymous_variant 0.14 rifampicin
rpoB 762245 c.2439G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762308 c.2502G>C synonymous_variant 0.11 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.12 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.13 rifampicin
rpoC 762374 c.-996G>C upstream_gene_variant 0.14 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.12 rifampicin Uncertain significance
rpoB 762920 c.3114C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763588 c.219C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763615 c.246G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>T synonymous_variant 0.24 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763900 c.531G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764344 c.975C>T synonymous_variant 0.16 rifampicin
rpoC 764353 c.984G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 765979 c.2610C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766381 c.3012C>T synonymous_variant 0.14 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.15 rifampicin
rpoC 766390 c.3021C>T synonymous_variant 0.16 rifampicin
rpoC 766393 c.3024C>T synonymous_variant 0.85 rifampicin Not assoc w R - Interim
rpoC 766741 c.3372G>C synonymous_variant 0.12 rifampicin
rpoC 767002 c.3633G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767008 c.3639G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767020 c.3651C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767221 c.3852C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800516 c.-293G>C upstream_gene_variant 0.12 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.12 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674348 c.147C>T synonymous_variant 0.98 isoniazid
ethionamide
inhA 1674924 c.723G>C synonymous_variant 0.22 isoniazid
ethionamide
inhA 1674930 c.729C>T synonymous_variant 0.22 isoniazid
ethionamide
inhA 1674934 c.733C>T synonymous_variant 0.16 isoniazid
ethionamide
rpsA 1833928 c.387G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.17 pyrazinamide
rpsA 1833979 c.438T>C 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
katG 2155696 p.Ala139Val missense_variant 0.14 isoniazid
katG 2155716 c.396T>G synonymous_variant 0.15 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.15 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.14 isoniazid
katG 2155742 p.Gly124Arg missense_variant 0.12 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518756 c.642G>C synonymous_variant 0.11 isoniazid
kasA 2519077 c.963G>C synonymous_variant 0.15 isoniazid
Rv2477c 2782528 c.1515G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087699 p.Leu294Val missense_variant 0.13 cycloserine
ald 3087704 c.885T>C synonymous_variant 0.15 cycloserine
ald 3087716 c.897G>C synonymous_variant 0.12 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
lpqB 3624701 c.210T>G synonymous_variant 0.14 rifampicin
bedaquiline
lpqB 3624704 c.207G>C synonymous_variant 0.14 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625123 c.-213T>C upstream_gene_variant 0.14 rifampicin
bedaquiline
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877638 c.870T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.16 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878160 c.348C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878163 c.345C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038587 c.2118C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038602 c.2103G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.16 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.15 pyrazinamide
clpC1 4038647 c.2058T>G synonymous_variant 0.14 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.12 pyrazinamide
clpC1 4038660 p.Ser682Cys missense_variant 0.12 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038671 c.2034T>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4038679 p.Pro676Ala missense_variant 0.16 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.12 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038725 c.1980C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038842 c.1863G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038941 c.1764G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.17 pyrazinamide
clpC1 4039067 c.1638G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.13 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039118 c.1587C>A synonymous_variant 0.14 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.18 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039169 c.1536A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039241 c.1464G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.15 pyrazinamide
clpC1 4040306 c.399G>C synonymous_variant 0.12 pyrazinamide
clpC1 4040309 c.396C>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4040324 c.381G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.17 pyrazinamide
clpC1 4040657 c.48T>G synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
glpK 4138757 c.999A>G synonymous_variant 0.12 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138763 c.993G>A synonymous_variant 0.14 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138769 c.987G>A synonymous_variant 0.13 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247527 c.1014G>C synonymous_variant 0.19 ethambutol
embB 4247536 c.1023C>A synonymous_variant 0.16 ethambutol
embB 4247554 c.1041T>C synonymous_variant 0.13 ethambutol
embB 4247555 p.Leu348Ile missense_variant 0.13 ethambutol
whiB6 4338497 p.Ala9Ser missense_variant 1.0 kanamycin Uncertain significance
capreomycin
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
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R