TB-Profiler result

Run: SRR1049042
Summary

Run ID: SRR1049042

Sample name:

Date: 02-04-2023 17:52:38

Number of reads: 2387210

Percentage reads mapped: 99.1

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 761128 p.Ser441Trp missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2288868 p.Val125Asp missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
ethA 4327084 c.380_389dupGCGCCCTCAC frameshift_variant 1.0 ethionamide
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
rpoB 761817 p.Arg671Gly missense_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
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 1.0
thyX 3067954 c.-9G>A upstream_gene_variant 1.0
thyA 3074186 c.285dupT frameshift_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.98
Rv3083 3449656 p.Ala385Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
ubiA 4269296 p.Met180Val missense_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408099 p.Leu35Arg missense_variant 0.96
gid 4408366 c.-164C>T upstream_gene_variant 0.98
katG 2153435 c.1120_*453del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0
thyA 3071514 c.365_*2165del frameshift_variant&stop_lost&splice_region_variant 1.0