TB-Profiler result

Run: SRR6856026
Summary

Run ID: SRR6856026

Sample name:

Date: 04-04-2023 17:53:44

Number of reads: 986694

Percentage reads mapped: 99.71

Strain: lineage4.4.1.1;lineage4.3.3

Drug-resistance: HR-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 0.51
lineage4.4 Euro-American S;T None 0.43
lineage4.4.1 Euro-American (S-type) S;T None 0.43
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.56
lineage4.4.1.1 Euro-American S;Orphans None 0.47
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
fabG1 1673432 c.-8T>A upstream_gene_variant 0.54 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.44 isoniazid
ethA 4327484 c.-11A>G upstream_gene_variant 0.54 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 8040 p.Gly247Ser missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619721 c.-170A>G upstream_gene_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.54
PPE35 2169840 p.Gly258Asp missense_variant 0.51
Rv1979c 2222341 p.Met275Thr missense_variant 0.35
Rv1979c 2223051 p.Glu38Asp missense_variant 0.63
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.5
Rv2752c 3065824 p.Pro123Leu missense_variant 0.53
thyA 3073868 p.Thr202Ala missense_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.51
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.39
fbiB 3641010 c.-525C>T upstream_gene_variant 0.55
clpC1 4038287 c.2418C>T synonymous_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245512 c.2280G>C synonymous_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.49