TB-Profiler result

Run: SRR6982234

Summary

Run ID: SRR6982234

Sample name:

Date: 04-04-2023 18:31:16

Number of reads: 671475

Percentage reads mapped: 99.57

Strain: lineage4.1.1.3

Drug-resistance: RR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 0.11 rifampicin
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 5845 p.Lys202Asn missense_variant 0.12
gyrB 6525 p.Arg429Leu missense_variant 0.11
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 576619 p.His424Gln missense_variant 0.11
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766844 p.Arg1159Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776107 p.Leu792Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781586 c.27C>A synonymous_variant 0.12
fbiC 1302793 c.-138A>G upstream_gene_variant 0.11
fbiC 1304190 c.1260G>A synonymous_variant 0.18
Rv1258c 1406887 p.Leu152Met missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102122 c.921C>A synonymous_variant 0.13
ndh 2103225 c.-183A>C upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223299 c.-135G>T upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.28
folC 2746860 p.Ala247Ser missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475004 p.Pro333Gln missense_variant 0.14
fprA 3475132 p.Gln376Lys missense_variant 0.15
fprA 3475176 p.Lys390Asn missense_variant 0.12
Rv3236c 3612401 p.Ser239* stop_gained 0.13
Rv3236c 3612882 p.Ala79Ser missense_variant 0.13
clpC1 4040834 c.-130G>T upstream_gene_variant 0.12
embC 4240688 p.Leu276Met missense_variant 0.14
embC 4242197 p.Ala779Ser missense_variant 0.15
embC 4242492 p.Arg877Leu missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244528 c.1296G>C synonymous_variant 0.12
embA 4244859 p.Gly543Trp missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4246563 p.Leu17Trp missense_variant 0.1
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249479 p.Ala989Glu missense_variant 0.15
aftB 4267795 p.Ala348Ser missense_variant 0.12
aftB 4268662 p.Thr59Ala missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0