TB-Profiler result

Run: SRR5341223
Summary

Run ID: SRR5341223

Sample name:

Date: 21-10-2023 01:28:13

Number of reads: 7953132

Percentage reads mapped: 99.31

Strain: lineage4.2.2.2;lineage1.1.2

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 (0.14)
Isoniazid R fabG1 c.-15C>T (0.87), katG p.Ser315Thr (0.12)
Ethambutol R embB p.Met306Ile (0.12)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00), gid c.102delG (0.11)
Fluoroquinolones R gyrB p.Ala504Val (0.78)
Moxifloxacin R gyrB p.Ala504Val (0.78)
Ofloxacin R gyrB p.Ala504Val (0.78)
Levofloxacin R gyrB p.Ala504Val (0.78)
Ciprofloxacin R gyrB p.Ala504Val (0.78)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.87)
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 0.13
lineage1 Indo-Oceanic EAI RD239 0.87
lineage4.2 Euro-American H;T;LAM None 0.14
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.87
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.14
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.87
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.11
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
gyrB 6750 p.Ala504Val missense_variant 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.14 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.87 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.12 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.12 ethambutol
gid 4408100 c.102delG frameshift_variant 0.11 streptomycin
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 5965 c.726A>G synonymous_variant 0.16
gyrB 6112 p.Met291Ile missense_variant 0.84
gyrB 6124 c.885C>T synonymous_variant 0.83
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.86
gyrA 8688 p.Ala463Ser missense_variant 0.12
gyrA 9047 c.1746C>T synonymous_variant 0.83
gyrA 9143 c.1842T>C synonymous_variant 0.79
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9328 p.Ala676Val missense_variant 0.17
gyrA 9443 c.2142G>A synonymous_variant 0.81
fgd1 491742 c.960T>C synonymous_variant 0.84
mshA 576000 p.Asp218Ala missense_variant 0.84
rpoB 760490 c.684C>T synonymous_variant 0.91
rpoB 761489 c.1683G>A synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
rpoC 763884 p.Ala172Val missense_variant 0.86
rpoC 763886 c.517C>A synonymous_variant 0.87
rpoC 765171 p.Pro601Leu missense_variant 0.91
rpoC 766485 p.Val1039Gly missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.81
mmpL5 776395 p.Phe696Leu missense_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.81
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 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.85
PPE35 2167983 p.Gly877Asp missense_variant 0.85
Rv1979c 2222308 p.Asp286Gly missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.91
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91
Rv2752c 3064632 c.1560C>T synonymous_variant 0.87
Rv2752c 3065305 p.Ala296Val missense_variant 0.89
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.13
ald 3086742 c.-78A>C upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.87
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.89
fprA 3475159 p.Asn385Asp missense_variant 0.9
ddn 3987057 p.Arg72Trp missense_variant 0.88
clpC1 4040517 p.Val63Ala missense_variant 0.89
embC 4240671 p.Thr270Ile missense_variant 0.75
embC 4241042 p.Asn394Asp missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.82
embA 4245969 p.Pro913Ser missense_variant 0.87
embB 4247646 p.Glu378Ala missense_variant 0.84
ubiA 4269387 p.Glu149Asp missense_variant 0.85
aftB 4269606 c.-770T>C upstream_gene_variant 0.89
whiB6 4338513 c.9C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.88
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407873 c.330G>T synonymous_variant 0.92