TB-Profiler result

Run: SRR24114357

Summary

Run ID: SRR24114357

Sample name:

Date: 22-04-2023 02:10:07

Number of reads: 3974110

Percentage reads mapped: 99.64

Strain: lineage3.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG c.1706_1707insT (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.390_391dupGG (1.00), pncA c.390_391dupGG (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2154405 c.1706_1707insT frameshift_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576113 p.Arg256Gly missense_variant 0.24
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761112 c.1308_1310delGAA disruptive_inframe_deletion 1.0
rpoB 761161 p.Leu452Arg missense_variant 0.19
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778944 c.-464C>A upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.12
rrl 1475550 n.1893A>T non_coding_transcript_exon_variant 0.13
fabG1 1673553 p.Asp38Glu missense_variant 0.17
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
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
ahpC 2726116 c.-77T>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.64
fbiD 3339751 p.Ala212Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.25
rpoA 3878601 c.-94C>G upstream_gene_variant 0.25
rpoA 3878630 c.-123G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.41
embC 4240409 p.Pro183Ala missense_variant 0.3
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243198 c.-34delC upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.23
embB 4246629 p.Val39Gly missense_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338662 c.-141G>A upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407716 p.Lys163Gln missense_variant 1.0