TB-Profiler result

Run: SRR18593214

Summary

Run ID: SRR18593214

Sample name:

Date: 03-04-2023 19:56:27

Number of reads: 3821337

Percentage reads mapped: 98.98

Strain: lineage4.2.2.2;lineage2.2

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
lineage2 East-Asian Beijing RD105 0.08
lineage4 Euro-American LAM;T;S;X;H None 0.91
lineage4.2 Euro-American H;T;LAM None 0.9
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.09
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.91
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.89
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 761139 p.His445Asp missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.1 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.89 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid
katG 2155841 p.Trp91Arg missense_variant 0.94 isoniazid
pncA 2289001 p.Phe81Val missense_variant 0.94 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 0.83 cycloserine
embB 4247429 p.Met306Val missense_variant 0.1 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 7581 p.Asp94Thr missense_variant 0.88
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.92
ccsA 620625 p.Ile245Met missense_variant 0.1
rpoB 761489 c.1683G>A synonymous_variant 0.9
rpoC 764585 p.Leu406Phe missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.17
mmpL5 776182 p.Asp767Asn missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715400 c.-68C>T upstream_gene_variant 0.9
ahpC 2726142 c.-51G>A upstream_gene_variant 0.95
pepQ 2860556 c.-138C>T upstream_gene_variant 0.86
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.95
ald 3086742 c.-78A>C upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448850 p.Trp116* stop_gained 0.88
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.11
ethA 4326773 p.Ala234Asp missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.1
gid 4407927 p.Glu92Asp missense_variant 0.11