TB-Profiler result

Run: ERR11243543
Summary

Run ID: ERR11243543

Sample name:

Date: 21-04-2023 21:27:08

Number of reads: 486849

Percentage reads mapped: 99.61

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr142Met (1.00)
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (1.00)
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 0.99
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8550 p.Ala417Thr missense_variant 0.15
gyrA 8560 p.Gly420Val missense_variant 0.14
gyrA 9275 p.Glu658Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490968 c.186C>T synonymous_variant 0.11
fgd1 491121 p.Glu113Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576209 p.Ala288Pro missense_variant 0.22
mshA 576616 c.1269G>C synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761161 c.1359delG frameshift_variant 0.17
rpoB 761814 p.Ala670Ser missense_variant 0.18
rpoB 762893 p.His1029Gln missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763896 p.Lys176Arg missense_variant 0.2
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 765995 p.Arg876Cys missense_variant 0.1
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 778318 p.Thr55Ala missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781646 p.Gln29His missense_variant 0.11
rpsL 781855 p.Arg99His missense_variant 0.15
rplC 800694 c.-115C>T upstream_gene_variant 0.12
fbiC 1302818 c.-113G>T upstream_gene_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406816 p.Trp175Cys missense_variant 0.17
embR 1417036 c.312C>T synonymous_variant 0.18
embR 1417391 c.-44C>G upstream_gene_variant 0.12
atpE 1460858 c.-187C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674108 c.-94C>T upstream_gene_variant 0.17
inhA 1674782 p.Ile194Asn missense_variant 0.13
inhA 1674858 p.Glu219Asp missense_variant 0.14
rpsA 1833397 c.-145G>T upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103217 c.-175C>A upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155632 c.480A>G synonymous_variant 0.17
PPE35 2167916 p.Phe899Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168482 p.Val711Ile missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2222377 p.Val263Asp missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518526 c.416delC frameshift_variant 0.22
folC 2746405 c.1194C>T synonymous_variant 0.25
thyA 3073714 p.Pro253Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087467 c.648C>T synonymous_variant 0.12
ald 3087527 c.712delG frameshift_variant 0.17
fbiD 3339714 c.597C>T synonymous_variant 0.22
Rv3083 3448927 p.Tyr142Asp missense_variant 0.12
Rv3083 3448982 p.Gly160Asp missense_variant 0.2
Rv3083 3449858 p.Pro452Leu missense_variant 0.15
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474983 p.Gly326Val missense_variant 0.25
whiB7 3568831 c.-152C>T upstream_gene_variant 0.13
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640497 c.-46G>T upstream_gene_variant 0.14
alr 3841259 c.162G>A synonymous_variant 0.15
alr 3841380 p.Thr14Met missense_variant 0.11
clpC1 4039307 c.1397delA frameshift_variant 0.5
clpC1 4040461 p.Pro82Ser missense_variant 0.1
embC 4240785 p.Gly308Val missense_variant 0.13
embC 4241264 p.Gly468Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248898 c.2386delC frameshift_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269640 c.193delG frameshift_variant 0.2
ethA 4326226 c.1248C>T synonymous_variant 0.13
ethA 4326651 p.Gly275Arg missense_variant 0.11
ethA 4326705 p.Pro257Ser missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407698 p.Asp169Tyr missense_variant 0.13
gid 4407927 p.Glu92Asp missense_variant 1.0