TB-Profiler result

Run: ERR4799454
Summary

Run ID: ERR4799454

Sample name:

Date: 20-10-2023 03:52:35

Number of reads: 2461750

Percentage reads mapped: 99.32

Strain: lineage1.2.2.2

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 (1.00)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.94)
Pyrazinamide R pncA p.Phe81Val (0.97)
Streptomycin R gid c.102delG (0.93)
Fluoroquinolones R gyrA p.Asp94Gly (0.97)
Moxifloxacin R gyrA p.Asp94Gly (0.97)
Ofloxacin R gyrA p.Asp94Gly (0.97)
Levofloxacin R gyrA p.Asp94Gly (0.97)
Ciprofloxacin R gyrA p.Asp94Gly (0.97)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyA c.-1323_*2870del (0.94)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.98
lineage1.2.2.2 Indo-Oceanic NA RD239 0.97
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 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289001 p.Phe81Val missense_variant 0.97 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.94 ethambutol
gid 4408100 c.102delG frameshift_variant 0.93 streptomycin
thyA 3070809 c.-1323_*2870del transcript_ablation 0.94 para-aminosalicylic_acid
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 5075 c.-165C>T upstream_gene_variant 0.95
gyrB 5670 p.Tyr144Phe missense_variant 0.94
gyrB 6112 p.Met291Ile missense_variant 0.98
gyrA 7268 c.-34C>T upstream_gene_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.96
rpoB 762423 p.Ile873Phe missense_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 0.95
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
embR 1417019 p.Cys110Tyr missense_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918245 c.306C>T synonymous_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.99
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9
ahpC 2726287 p.Gly32Asp missense_variant 0.97
Rv2752c 3066274 c.-83A>C upstream_gene_variant 0.98
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.97
fprA 3474698 p.Asp231Gly missense_variant 0.97
fprA 3475159 p.Asn385Asp missense_variant 0.98
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240671 p.Thr270Ile missense_variant 0.98
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.94
embB 4247646 p.Glu378Ala missense_variant 0.99
ubiA 4269387 p.Glu149Asp missense_variant 0.93
aftB 4269606 c.-770T>C upstream_gene_variant 0.98
ethA 4326148 c.1326G>T synonymous_variant 0.98
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.95
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.96