TB-Profiler result

Run: SRR25827883
Summary

Run ID: SRR25827883

Sample name:

Date: 03-02-2024 00:13:02

Number of reads: 6864269

Percentage reads mapped: 99.1

Strain: lineage4.2.2.2;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.Asp435Tyr (0.55), rpoB p.Ser450Leu (0.48)
Isoniazid R katG p.Ser315Thr (0.47), katG c.707_708delAC (0.53), ahpC c.-48G>A (0.48)
Ethambutol R embB p.Gly406Ala (0.37), embB p.Asp1024Asn (0.50)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.47)
Fluoroquinolones R gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51)
Moxifloxacin R gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51)
Ofloxacin R gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51)
Levofloxacin R gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51)
Ciprofloxacin R gyrA p.Ala90Val (0.47), gyrA p.Asp94Gly (0.51)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Cys253* (0.46)
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 0.55
lineage4 Euro-American LAM;T;S;X;H None 0.48
lineage4.2 Euro-American H;T;LAM None 0.47
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.44
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.43
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 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.51 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.55 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.48 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.47 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.47 isoniazid
katG 2155403 c.707_708delAC frameshift_variant 0.53 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.48 isoniazid
embB 4247730 p.Gly406Ala missense_variant 0.37 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.5 ethambutol
ethA 4326715 p.Cys253* stop_gained 0.46 ethionamide
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 8025 p.Asp242His missense_variant 0.52
gyrA 8158 p.Ser286Leu missense_variant 0.54
gyrA 8688 p.Ala463Ser missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.6
mshA 576077 c.730C>T synonymous_variant 0.48
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoB 761489 c.1683G>A synonymous_variant 0.48
rpoC 762434 c.-936T>G upstream_gene_variant 0.52
rpoC 763031 c.-339T>C upstream_gene_variant 0.51
rpoC 764916 p.Leu516Pro missense_variant 0.48
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpR5 779393 p.Arg135Gln missense_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305050 p.Thr707Met missense_variant 0.43
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476561 n.2904C>T non_coding_transcript_exon_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.61
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.45
pncA 2289365 c.-125delC upstream_gene_variant 0.56
ahpC 2726105 c.-88G>A upstream_gene_variant 0.53
ahpC 2726116 c.-77T>G upstream_gene_variant 0.53
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.39
ald 3086742 c.-78A>C upstream_gene_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.14
whiB7 3568428 c.252A>C synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.64
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.19
whiB6 4338399 p.Trp41Cys missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.59
gid 4408093 p.Gly37Glu missense_variant 0.53