TB-Profiler result

Run: SRR25827488
Summary

Run ID: SRR25827488

Sample name:

Date: 02-02-2024 05:23:37

Number of reads: 10347093

Percentage reads mapped: 98.8

Strain: lineage4.3.3;lineage1.2.2.2

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 (0.69), rpoB p.Ile491Phe (0.34)
Isoniazid R katG p.Ser315Thr (1.00), katG c.72_73dupTC (0.25)
Ethambutol
Pyrazinamide R pncA p.Ile5Ser (0.12)
Streptomycin R rpsL p.Lys43Arg (0.48)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.13)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 0.35
lineage1 Indo-Oceanic EAI RD239 0.5
lineage4.3 Euro-American (LAM) mainly-LAM None 0.34
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.5
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.34
lineage1.2.2.2 Indo-Oceanic NA RD239 0.52
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 0.69 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.34 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.48 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2156038 c.72_73dupTC frameshift_variant 0.25 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.12 pyrazinamide
thyA 3074408 p.Thr22Ala missense_variant 0.13 para-aminosalicylic_acid
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 5075 c.-165C>T upstream_gene_variant 0.49
gyrB 5201 c.-39A>G upstream_gene_variant 0.56
gyrB 6112 p.Met291Ile missense_variant 0.47
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.51
gyrA 7268 c.-34C>T upstream_gene_variant 0.47
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.38
gyrA 8452 p.Ala384Val missense_variant 0.5
gyrA 9143 c.1842T>C synonymous_variant 0.54
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.66
mshA 575907 p.Ala187Val missense_variant 0.19
rpoB 761276 c.1470G>T synonymous_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 0.62
rpoC 763884 p.Ala172Val missense_variant 0.47
rpoC 763886 c.517C>A synonymous_variant 0.47
rpoC 764995 c.1626C>G synonymous_variant 0.37
rpoC 765862 p.Phe831Leu missense_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.66
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406170 p.Gly391Arg missense_variant 0.49
Rv1258c 1406760 c.580_581insC frameshift_variant 0.16
embR 1417019 p.Cys110Tyr missense_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471754 n.-92T>G upstream_gene_variant 0.48
rpsA 1834177 c.636A>C synonymous_variant 0.13
rpsA 1834836 p.Met432Thr missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101756 c.1287G>T synonymous_variant 0.61
katG 2154724 p.Arg463Leu missense_variant 0.69
katG 2156196 c.-85C>T upstream_gene_variant 0.32
PPE35 2167926 p.Leu896Ser missense_variant 0.7
PPE35 2168742 p.Gly624Asp missense_variant 0.59
Rv1979c 2222308 p.Asp286Gly missense_variant 0.56
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pncA 2289069 p.Phe58Cys missense_variant 0.37
kasA 2518132 c.18C>T synonymous_variant 0.5
kasA 2518919 p.Gly269Ser missense_variant 0.33
eis 2714177 p.Leu386Ile missense_variant 0.48
ahpC 2726051 c.-142G>A upstream_gene_variant 0.52
folC 2746340 p.Ala420Val missense_variant 0.42
thyX 3067949 c.-4C>T upstream_gene_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.52
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.52
fprA 3475159 p.Asn385Asp missense_variant 0.55
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.38
clpC1 4040517 p.Val63Ala missense_variant 0.56
embC 4240671 p.Thr270Ile missense_variant 0.51
embC 4241042 p.Asn394Asp missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.16
embA 4245969 p.Pro913Ser missense_variant 0.51
embB 4247015 p.Ser168Ala missense_variant 0.21
embB 4247646 p.Glu378Ala missense_variant 0.56
embB 4247847 p.Gln445Arg missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 0.54
aftB 4269606 c.-770T>C upstream_gene_variant 0.54
ethA 4326148 c.1326G>T synonymous_variant 0.5
ethA 4326439 p.Asn345Lys missense_variant 0.53
whiB6 4338203 p.Arg107Cys missense_variant 0.65
whiB6 4338533 c.-12T>C upstream_gene_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.48
gid 4407588 c.615A>G synonymous_variant 0.63
gid 4407873 c.330G>T synonymous_variant 0.49
gid 4407927 p.Glu92Asp missense_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 0.35