TB-Profiler result

Run: SRR6832019
Summary

Run ID: SRR6832019

Sample name:

Date: 04-04-2023 17:10:29

Number of reads: 550456

Percentage reads mapped: 99.39

Strain: lineage4.2.1.1

Drug-resistance: MDR-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
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.99
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 761139 p.His445Asn missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 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 5312 p.Ala25Thr missense_variant 0.13
gyrB 6642 p.Lys468Arg missense_variant 0.33
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 759615 c.-192A>C upstream_gene_variant 0.5
rpoB 761279 p.Ile491Met missense_variant 1.0
rpoB 761610 p.Gly602Arg missense_variant 0.25
rpoC 765674 p.Glu769* stop_gained 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776635 p.Asp616Asn missense_variant 0.25
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 778963 c.-483G>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472259 n.414C>T non_coding_transcript_exon_variant 0.18
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.14
fabG1 1674076 p.Thr213Pro missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223345 c.-181T>A upstream_gene_variant 0.25
kasA 2518698 p.Cys195Tyr missense_variant 0.4
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449946 c.1443C>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877809 p.Glu233Asp missense_variant 0.18
panD 4044378 c.-97G>A upstream_gene_variant 0.18
embC 4241141 p.Ile427Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245318 p.Ile696Leu missense_variant 1.0
embB 4246982 p.Thr157Pro missense_variant 0.2
ethA 4326992 p.Ile161Asn missense_variant 0.33
ethR 4327258 c.-291C>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0