TB-Profiler result

Run: ERR11243566
Summary

Run ID: ERR11243566

Sample name:

Date: 21-04-2023 22:47:48

Number of reads: 493428

Percentage reads mapped: 99.56

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00), katG p.Met176Ile (0.20)
Ethambutol R embA c.-12C>T (1.00), embB p.Tyr334His (1.00)
Pyrazinamide R pncA p.His71Arg (1.00)
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155584 p.Met176Ile missense_variant 0.2 isoniazid
pncA 2289030 p.His71Arg missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 1.0 ethambutol
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
gyrB 5279 p.Ala14Ser missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8276 c.975G>A synonymous_variant 0.26
gyrA 8277 p.Val326Met missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9789 p.Ala830Ser missense_variant 0.15
fgd1 490597 c.-186G>T upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575992 c.645C>A synonymous_variant 0.13
mshA 576169 c.822C>A synonymous_variant 0.13
ccsA 619949 p.Ser20* stop_gained 0.14
ccsA 620029 p.Leu47Met missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759697 c.-110A>G upstream_gene_variant 0.11
rpoB 762292 p.Thr829Asn missense_variant 0.13
rpoB 762741 p.Leu979Met missense_variant 0.15
rpoB 763029 p.Ala1075Ser missense_variant 0.2
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767037 p.Ala1223Glu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777746 c.735G>T synonymous_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303458 c.528G>T synonymous_variant 0.15
fbiC 1305142 p.Glu738Lys missense_variant 0.22
Rv1258c 1406517 p.Ala275Glu missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407184 c.157C>T synonymous_variant 0.5
embR 1416770 p.Glu193Gly missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473981 n.324G>T non_coding_transcript_exon_variant 0.17
fabG1 1673267 c.-173C>A upstream_gene_variant 0.15
fabG1 1673393 c.-47G>T upstream_gene_variant 0.18
fabG1 1673638 p.Ala67Ser missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918215 c.276G>T synonymous_variant 0.18
katG 2154418 p.Val565Ala missense_variant 0.15
katG 2154673 p.Ala480Glu missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168944 p.Gln557Lys missense_variant 0.14
Rv1979c 2221918 p.Val416Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289239 c.3G>T start_lost 0.14
eis 2714766 c.567G>T synonymous_variant 0.22
Rv2752c 3067086 c.-895A>G upstream_gene_variant 0.11
thyA 3074573 c.-102C>G upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
fbiD 3339285 c.168G>C synonymous_variant 0.2
fbiD 3339693 c.576C>A synonymous_variant 0.2
Rv3083 3449946 c.1443C>A synonymous_variant 0.18
fprA 3473879 c.-128T>G upstream_gene_variant 0.15
fprA 3473927 c.-79delT upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612287 p.Gly277Val missense_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841272 p.Arg50Leu missense_variant 0.12
alr 3841512 c.-92C>A upstream_gene_variant 0.13
clpC1 4040778 c.-74G>T upstream_gene_variant 0.2
panD 4044147 c.135C>A synonymous_variant 0.18
embC 4241105 c.1246dupG frameshift_variant 0.22
embC 4241391 p.Leu510Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242913 c.-320C>A upstream_gene_variant 0.12
embA 4243385 c.153C>A synonymous_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245076 p.Ala615Glu missense_variant 0.29
embB 4245692 c.-822G>T upstream_gene_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268400 p.Ala146Asp missense_variant 0.13
aftB 4268493 p.Ala115Glu missense_variant 0.15
ubiA 4269535 p.Trp100* stop_gained 0.2
ethA 4328455 c.-982G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0