TB-Profiler result

Run: ERR025841
Summary

Run ID: ERR025841

Sample name:

Date: 31-03-2023 08:18:06

Number of reads: 457107

Percentage reads mapped: 99.05

Strain: lineage4.1.2.1

Drug-resistance: RR-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
lineage4.1.2 Euro-American T;H None 0.21
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.11
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 761155 p.Ser450Leu missense_variant 0.33 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin
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 5520 p.Pro94Leu missense_variant 0.23
gyrB 7121 p.Pro628Ala missense_variant 0.36
gyrA 7222 c.-80C>T upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9293 c.1992G>T synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490696 c.-87T>G upstream_gene_variant 0.25
mshA 576077 c.730C>T synonymous_variant 0.2
rpoB 759831 p.Thr9Pro missense_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 0.22
rpoC 764725 p.Phe452Leu missense_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406750 c.591C>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.38
inhA 1674892 p.Asn231Asp missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168366 c.2247G>A synonymous_variant 0.18
PPE35 2169866 c.747G>C synonymous_variant 0.12
Rv1979c 2222982 c.183G>T synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.38
pepQ 2860260 c.159G>A synonymous_variant 0.36
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.5
Rv2752c 3067012 c.-821C>G upstream_gene_variant 0.29
thyA 3073806 c.666C>G synonymous_variant 0.5
thyA 3074654 c.-183T>G upstream_gene_variant 0.25
ald 3086742 c.-78A>C upstream_gene_variant 0.57
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475348 p.Ala448Thr missense_variant 0.25
clpC1 4038319 p.Pro796Ala missense_variant 0.62
clpC1 4039932 p.Gly258Val missense_variant 0.25
embC 4242482 p.Asn874His missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.4
embC 4242806 p.Phe982Ile missense_variant 0.4
embC 4243045 p.Gln1061His missense_variant 0.4
embA 4243624 p.Ile131Ser missense_variant 0.33
embB 4246845 p.Leu111Ser missense_variant 0.18
ubiA 4269529 p.Ala102Gly missense_variant 0.29
ethA 4326996 p.Pro160Thr missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.33