TB-Profiler result

Run: SRR25827360
Summary

Run ID: SRR25827360

Sample name:

Date: 15-03-2024 10:39:19

Number of reads: 16432873

Percentage reads mapped: 99.07

Strain: lineage4;lineage3

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.His445Tyr (0.73), rpoB p.Ser450Leu (0.25)
Isoniazid R katG p.Ser315Thr (0.97)
Ethambutol R embB p.Gln497Lys (0.81)
Pyrazinamide
Streptomycin R gid p.Leu79Ser (0.14)
Fluoroquinolones R gyrA p.Asp94Gly (0.15)
Moxifloxacin R gyrA p.Asp94Gly (0.15)
Ofloxacin R gyrA p.Asp94Gly (0.15)
Levofloxacin R gyrA p.Asp94Gly (0.15)
Ciprofloxacin R gyrA p.Asp94Gly (0.15)
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
lineage3 East-African-Indian CAS RD750 0.82
lineage4 Euro-American LAM;T;S;X;H None 0.11
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
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 7582 p.Asp94Gly missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.73 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
embB 4248002 p.Gln497Lys missense_variant 0.81 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.14 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 6963 p.Arg575His missense_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 0.87
fgd1 491742 c.960T>C synonymous_variant 0.91
rpoB 759746 c.-61C>T upstream_gene_variant 0.81
rpoC 762434 c.-936T>G upstream_gene_variant 0.83
rpoB 762909 p.Ile1035Val missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 776181 p.Asp767Ala missense_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.84
ahpC 2726105 c.-88G>A upstream_gene_variant 0.84
ald 3086788 c.-32T>C upstream_gene_variant 0.89
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
alr 3841578 c.-158G>A upstream_gene_variant 0.73
alr 3841590 c.-170G>A upstream_gene_variant 0.79
embC 4242075 p.Arg738Gln missense_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.16
aftB 4268719 p.Asn40Asp missense_variant 0.74
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.89
gid 4408070 p.Trp45Arg missense_variant 0.78