TB-Profiler result

Run: ERR5865011
Summary

Run ID: ERR5865011

Sample name:

Date: 01-04-2023 23:44:18

Number of reads: 1420761

Percentage reads mapped: 98.7

Strain: lineage4

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
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
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620619 c.729G>A synonymous_variant 1.0
rpoC 767007 c.3640_3645dupTCGCTG conservative_inframe_insertion 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778090 p.Gly131Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
Rv1258c 1407448 c.-108C>T upstream_gene_variant 0.12
Rv1258c 1407509 c.-169C>A upstream_gene_variant 0.12
embR 1416966 p.Ala128Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 1.0
rrl 1474721 n.1064G>T non_coding_transcript_exon_variant 0.13
rrl 1475540 n.1883C>A non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154594 c.1518G>A synonymous_variant 1.0
PPE35 2168235 p.Ala793Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726156 c.-36delC upstream_gene_variant 0.11
Rv2752c 3064810 p.Thr461Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568819 c.-140C>G upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242835 c.-398C>T upstream_gene_variant 1.0
embA 4244852 c.1620G>T synonymous_variant 0.1
ethA 4327310 p.Ser55Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0