TB-Profiler result

Run: SRR6484891
Summary

Run ID: SRR6484891

Sample name:

Date: 04-04-2023 14:51:14

Number of reads: 1366958

Percentage reads mapped: 99.65

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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.25 streptomycin
katG 2155167 p.Ser315Arg missense_variant 0.31 isoniazid
ahpC 2726119 c.-74G>A upstream_gene_variant 0.86 isoniazid
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
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
fabG1 1673164 c.-276C>T upstream_gene_variant 1.0
fabG1 1673774 p.Asn112Thr missense_variant 0.25
rpsA 1834709 c.1169delA frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155217 p.Gly299Ser missense_variant 0.91
katG 2155828 p.Tyr95Cys missense_variant 0.13
PPE35 2168140 p.Ala825Ser missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3840375 p.Asp349Gly missense_variant 1.0
alr 3841539 c.-119C>T upstream_gene_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.17
rpoA 3878082 c.426T>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244362 p.Asn377Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407945 c.258C>T synonymous_variant 1.0
gid 4408030 c.172delC frameshift_variant 0.85
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0