TB-Profiler result

Run: ERR6866112
Summary

Run ID: ERR6866112

Sample name:

Date: 02-04-2023 03:15:56

Number of reads: 1738471

Percentage reads mapped: 99.63

Strain: lineage4.3.3;lineage4.1.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.2
lineage4.1 Euro-American T;X;H None 0.34
lineage4.1.2 Euro-American T;H None 0.35
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.22
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.29
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 1673423 c.-17G>T upstream_gene_variant 0.48 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.23 isoniazid
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 0.98
gyrA 8040 p.Gly247Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.15
mshA 575679 p.Asn111Ser missense_variant 0.48
rpoB 760106 c.300G>A synonymous_variant 0.35
rpoB 760115 c.309C>T synonymous_variant 0.38
rpoB 761889 p.Val695Leu missense_variant 0.46
rpoC 764995 c.1626C>G synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.54
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.61
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.28
kasA 2518919 p.Gly269Ser missense_variant 0.17
Rv2752c 3065517 c.675C>T synonymous_variant 0.51
thyA 3073868 p.Thr202Ala missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 0.57
Rv3083 3448439 c.-64delA upstream_gene_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.53
fprA 3474299 p.Asp98Gly missense_variant 0.57
fbiB 3641454 c.-81G>A upstream_gene_variant 0.36
rpoA 3878635 c.-128C>T upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.26
embC 4242182 p.Ala774Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
ethA 4328317 c.-844C>T upstream_gene_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 0.15