TB-Profiler result

Run: SRR3105741
Summary

Run ID: SRR3105741

Sample name:

Date: 04-04-2023 05:07:14

Number of reads: 4087901

Percentage reads mapped: 98.09

Strain: lineage4.2.1

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.5 kanamycin, amikacin
ahpC 2726141 c.-52C>T upstream_gene_variant 0.99 isoniazid
embB 4247429 p.Met306Leu missense_variant 0.99 ethambutol
embB 4248003 p.Gln497Pro 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 6610 c.-692C>G upstream_gene_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575504 p.His53Asp missense_variant 0.51
mshA 576057 c.711_712dupGG frameshift_variant 0.4
rpoC 767123 p.Val1252Met missense_variant 1.0
rpoC 767314 p.Tyr1315* stop_gained 0.28
mmpL5 775639 p.Ile948Val 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 1472512 n.667A>G non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169830 c.783C>T synonymous_variant 0.11
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223284 c.-120C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289162 p.Leu27Arg missense_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612746 c.370delG frameshift_variant 1.0
fbiB 3642772 p.Asp413Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.27
aftB 4267823 c.1014G>C synonymous_variant 0.99
ethA 4327349 p.Gly42Ala missense_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408149 c.54T>C synonymous_variant 1.0