TB-Profiler result

Run: SRR1172140
Summary

Run ID: SRR1172140

Sample name:

Date: 03-04-2023 02:57:42

Number of reads: 977695

Percentage reads mapped: 98.57

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_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
gyrB 5608 c.369C>T synonymous_variant 0.95
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9073 p.Ala591Glu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575741 p.Phe132Leu missense_variant 0.11
rpoB 762539 p.Leu911Phe missense_variant 0.12
rpoB 762889 p.His1028Arg missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781525 c.-35A>G upstream_gene_variant 0.1
rpsL 781911 p.Gly118Cys missense_variant 0.11
fbiC 1303005 c.75G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.12
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.12
fabG1 1673504 p.Gly22Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155160 p.Glu318Lys missense_variant 0.11
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747744 c.-146A>G upstream_gene_variant 0.11
ribD 2987559 p.Ala241Ser missense_variant 0.1
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448649 p.Arg49Leu missense_variant 0.11
Rv3083 3448835 p.Ser111Ile missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640852 p.Leu104Ile missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044032 p.Leu84Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247007 p.Lys165Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0