TB-Profiler result

Run: SRR6650149
Summary

Run ID: SRR6650149

Sample name:

Date: 15-08-2023 07:59:26

Number of reads: 3679029

Percentage reads mapped: 99.67

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
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide
Streptomycin R gid c.115delC (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 6922 c.-380G>T upstream_gene_variant 0.16
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.2
ccsA 620756 p.Asp289Gly missense_variant 0.17
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779363 p.Leu125Arg missense_variant 0.18
mmpR5 779371 p.Ala128Pro missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.2
fbiC 1304146 p.Ile406Val missense_variant 0.17
atpE 1461086 c.42A>G synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474479 n.822A>C non_coding_transcript_exon_variant 0.15
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918052 p.Pro38Arg missense_variant 0.15
tlyA 1918059 c.120C>A synonymous_variant 0.21
ndh 2103225 c.-183A>C upstream_gene_variant 0.27
ndh 2103235 c.-193C>G upstream_gene_variant 0.21
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.17
ahpC 2726341 p.Val50Gly missense_variant 0.2
ahpC 2726345 c.153C>T synonymous_variant 0.19
ahpC 2726350 p.Trp53Leu missense_variant 0.22
ribD 2987323 p.Val162Gly missense_variant 0.18
thyA 3074641 c.-170C>T upstream_gene_variant 0.16
thyA 3074648 c.-177T>G upstream_gene_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.2
embC 4240061 p.Phe67Val missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.17
embC 4242414 p.Leu851Arg missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0