TB-Profiler result

Run: ERR2652993
Summary

Run ID: ERR2652993

Sample name:

Date: 31-03-2023 22:26:07

Number of reads: 475141

Percentage reads mapped: 96.6

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 None 0.96
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 0.96 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.94 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.11 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326109 c.1363_1364delTG frameshift_variant 0.15 ethionamide
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
mshA 576123 p.Leu259Arg missense_variant 0.17
rpoC 764298 p.Met310Thr missense_variant 0.12
rpoC 764558 p.Arg397Cys missense_variant 0.11
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765996 p.Arg876His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 1.0
mmpL5 779244 c.-764G>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303487 p.Gly186Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.17
rrs 1472998 n.1153C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102840 c.202delA frameshift_variant 0.12
katG 2155012 p.Pro367Gln missense_variant 0.18
PPE35 2167881 p.Asn911Ser missense_variant 0.14
Rv1979c 2221783 p.Ala461Gly missense_variant 0.13
Rv1979c 2222697 c.468C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289070 p.Phe58Val missense_variant 0.93
pncA 2290179 c.-938G>A upstream_gene_variant 0.12
fbiD 3339535 p.Val140Ile missense_variant 0.12
Rv3083 3448669 p.Asp56Asn missense_variant 0.12
Rv3083 3449448 c.945G>A synonymous_variant 0.13
alr 3841071 p.Gly117Asp missense_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 0.13
clpC1 4040525 c.180C>T synonymous_variant 1.0
clpC1 4040621 c.84C>A synonymous_variant 0.17
embC 4240599 c.739delG frameshift_variant 0.14
embC 4241289 p.Ile476Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Thr missense_variant 1.0
embA 4244798 c.1566G>A synonymous_variant 0.17
embA 4245703 p.Ser824Trp missense_variant 0.11
embB 4249732 c.3219C>G synonymous_variant 0.95
ethA 4327295 p.Tyr60Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407590 p.Ala205Thr missense_variant 1.0