TB-Profiler result

Run: SRR17657949
Summary

Run ID: SRR17657949

Sample name:

Date: 12-01-2024 03:46:38

Number of reads: 2399766

Percentage reads mapped: 99.6

Strain: lineage4.3.4.2.1;lineage1.1.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00), ahpC c.-48G>A (0.51)
Ethambutol R embB p.Met306Ile (0.53), embB p.Gln497Arg (0.53)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
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 0.6
lineage1 Indo-Oceanic EAI RD239 0.43
lineage4.3 Euro-American (LAM) mainly-LAM None 0.58
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.47
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.4
lineage4.3.4 Euro-American (LAM) LAM RD174 0.59
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.54
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.59
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.51 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.53 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.53 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 6112 p.Met291Ile missense_variant 0.51
gyrB 6124 c.885C>T synonymous_variant 0.5
gyrB 6140 p.Val301Leu missense_variant 0.42
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.57
gyrA 9143 c.1842T>C synonymous_variant 0.35
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 0.36
rpoC 763884 p.Ala172Val missense_variant 0.48
rpoC 763886 c.517C>A synonymous_variant 0.46
rpoC 764995 c.1626C>G synonymous_variant 0.64
rpoC 765171 p.Pro601Leu missense_variant 0.56
rpoC 765312 p.Ala648Asp missense_variant 0.49
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.51
mmpS5 778696 c.206_209dupTCAA frameshift_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304743 p.Ile605Val missense_variant 0.46
embR 1417019 p.Cys110Tyr missense_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.32
katG 2154953 p.Asp387His missense_variant 0.53
PPE35 2167926 p.Leu896Ser missense_variant 0.46
PPE35 2167983 p.Gly877Asp missense_variant 0.56
Rv1979c 2222308 p.Asp286Gly missense_variant 0.61
Rv1979c 2222641 p.Ser175Leu missense_variant 0.64
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289781 c.-540C>A upstream_gene_variant 0.43
kasA 2518132 c.18C>T synonymous_variant 0.57
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41
folC 2746258 c.1341C>T synonymous_variant 0.32
folC 2746488 p.Asp371Tyr missense_variant 0.33
pepQ 2860017 c.402T>C synonymous_variant 0.7
Rv2752c 3064632 c.1560C>T synonymous_variant 0.38
thyA 3073868 p.Thr202Ala missense_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.41
Rv3083 3448721 p.Lys73Thr missense_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.44
fprA 3475159 p.Asn385Asp missense_variant 0.46
Rv3236c 3612009 p.Ala370Thr missense_variant 0.64
alr 3840719 c.702A>G synonymous_variant 0.59
clpC1 4038287 c.2418C>T synonymous_variant 0.62
clpC1 4040517 p.Val63Ala missense_variant 0.5
embC 4240671 p.Thr270Ile missense_variant 0.38
embC 4241042 p.Asn394Asp missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243245 p.Gly5Arg missense_variant 0.36
embA 4243848 p.Val206Met missense_variant 0.33
embA 4244148 p.Trp306Arg missense_variant 0.54
embA 4245969 p.Pro913Ser missense_variant 0.4
embB 4247646 p.Glu378Ala missense_variant 0.47
ubiA 4269387 p.Glu149Asp missense_variant 0.54
aftB 4269606 c.-770T>C upstream_gene_variant 0.38
ethA 4326113 p.Pro454Leu missense_variant 0.49
ethA 4326953 p.Asp174Gly missense_variant 0.55
whiB6 4338289 p.Gly78Glu missense_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.57
gid 4407588 c.615A>G synonymous_variant 0.67
gid 4407873 c.330G>T synonymous_variant 0.41
gid 4408125 p.Leu26Phe missense_variant 0.55
gid 4408156 p.Leu16Arg missense_variant 0.5