TB-Profiler result

Run: SRR6896326
Summary

Run ID: SRR6896326

Sample name:

Date: 04-04-2023 18:02:24

Number of reads: 604849

Percentage reads mapped: 99.53

Strain: lineage4.1.1.3

Drug-resistance: Other

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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 0.99
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
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
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 762841 c.3036_3037delGT frameshift_variant 0.18
rpoC 764305 p.Met312Ile missense_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766413 p.Phe1015Ser missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
atpE 1461241 p.Ile66Asn missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471729 n.-117T>C upstream_gene_variant 0.12
inhA 1674652 p.Pro151Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167975 p.Ala880Thr missense_variant 0.13
PPE35 2168709 p.Asn635Ser missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
PPE35 2170298 c.315A>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290131 c.-890G>A upstream_gene_variant 0.17
eis 2715578 c.-246C>G upstream_gene_variant 0.11
pepQ 2859493 p.Gly309Val missense_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339538 p.Ala141Thr missense_variant 0.1
fprA 3473941 c.-66A>C upstream_gene_variant 0.13
fprA 3473944 c.-63A>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475239 c.1233A>G synonymous_variant 0.11
fprA 3475372 p.Gly456Ser missense_variant 0.11
fbiB 3641593 p.Leu20Pro missense_variant 0.14
fbiB 3641605 p.Arg24Leu missense_variant 0.12
fbiB 3641770 p.Glu79Gly missense_variant 0.11
fbiB 3642070 p.Val179Ala missense_variant 0.12
fbiB 3642104 c.570C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243790 c.558G>T synonymous_variant 0.12
embA 4244285 c.1053G>T synonymous_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267368 p.Asn490Ser missense_variant 0.1
aftB 4267838 c.999T>C synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0
gid 4408160 p.Arg15Trp missense_variant 0.11