TB-Profiler result

Run: SRR1165529
Summary

Run ID: SRR1165529

Sample name:

Date: 03-04-2023 00:27:04

Number of reads: 3190631

Percentage reads mapped: 99.47

Strain: lineage4.7

Drug-resistance: MDR-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
lineage4.7 Euro-American (mainly T) T1;T5 None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288727 c.513_514dupGC frameshift_variant 0.9 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val 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
rpoC 763960 c.591T>G synonymous_variant 0.13
rpoC 764725 p.Phe452Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304121 c.1191A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471861 n.16T>A non_coding_transcript_exon_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170251 p.Val121Ala missense_variant 0.12
PPE35 2170336 p.Met93Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3236c 3612493 c.624G>A synonymous_variant 1.0
fbiB 3641951 c.417G>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4267500 p.Pro446Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407746 p.Ile153Val missense_variant 1.0
gid 4407745 c.-397_457del frameshift_variant&start_lost 1.0