TB-Profiler result

Run: SRR6824331
Summary

Run ID: SRR6824331

Sample name:

Date: 04-04-2023 16:27:37

Number of reads: 10211749

Percentage reads mapped: 99.06

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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 761110 p.Asp435Val missense_variant 0.77 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin
katG 2154857 p.Asp419His missense_variant 0.31 isoniazid
pncA 2288827 p.Val139Leu missense_variant 0.74 pyrazinamide
pncA 2289141 p.Tyr34Ser missense_variant 0.21 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 0.21 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.57 isoniazid
embB 4247429 p.Met306Val missense_variant 0.18 ethambutol
embB 4248002 p.Gln497Lys missense_variant 0.79 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575906 p.Ala187Thr missense_variant 1.0
rpoB 759940 p.Pro45Gln missense_variant 0.25
rpoC 764500 c.1131C>T synonymous_variant 1.0
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 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.13
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.15
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.16
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.11
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.11
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.11
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.11
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.11
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448727 p.Leu75Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613172 c.-56C>T upstream_gene_variant 1.0
clpC1 4039058 p.Phe549Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243991 c.759T>G synonymous_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0