TB-Profiler result

Run: SRR7592354

Summary

Run ID: SRR7592354

Sample name:

Date: 04-04-2023 19:49:33

Number of reads: 2166491

Percentage reads mapped: 99.26

Strain: lineage4.8

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
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 2155168 p.Ser315Ile missense_variant 1.0 isoniazid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
pncA 2289010 c.152_231delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG frameshift_variant 1.0 pyrazinamide
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
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576113 p.Arg256Gly missense_variant 0.23
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ald 3086987 p.Gln56His missense_variant 0.98
ald 3087455 c.638delG frameshift_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.55
fbiD 3339746 p.Ala210Gly missense_variant 0.31
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.3
rpoA 3878613 c.-106A>C upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.4
embC 4240409 p.Pro183Ala missense_variant 0.18
embC 4241555 p.Ser565Gly missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.27
embB 4246584 p.Arg24Pro missense_variant 0.35
embB 4248004 p.Gln497His missense_variant 1.0
ethA 4326299 p.Thr392Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0