TB-Profiler result

Run: SRR5341360
Summary

Run ID: SRR5341360

Sample name:

Date: 20-10-2023 18:51:04

Number of reads: 2054642

Percentage reads mapped: 93.39

Strain: 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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ala (0.94)
Pyrazinamide R pncA p.Val180Ala (0.86)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Ala504Val (0.86), gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrB p.Ala504Val (0.86), gyrA p.Ala90Val (1.00)
Ofloxacin R gyrB p.Ala504Val (0.86), gyrA p.Ala90Val (1.00)
Levofloxacin R gyrB p.Ala504Val (0.86), gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrB p.Ala504Val (0.86), gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA p.Lys69Glu (1.00)
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 1.0
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 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
tlyA 1918144 p.Lys69Glu missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288703 p.Val180Ala missense_variant 0.86 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.94 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761074 p.Glu423Gly missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764023 c.654G>A synonymous_variant 1.0
rpoC 765113 p.Val582Leu missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168565 p.Pro683Leu missense_variant 0.91
PPE35 2170599 p.Val5Ala missense_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987013 p.Ser59Gly missense_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
fprA 3474661 p.Asp219Asn missense_variant 0.91
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4328192 p.Asn215Ile missense_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0