TB-Profiler result

Run: ERR6358762
Summary

Run ID: ERR6358762

Sample name:

Date: 02-04-2023 02:13:22

Number of reads: 7809185

Percentage reads mapped: 99.73

Strain: lineage4.8.1;lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 0.54
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.49
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.49
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.5
lineage4.6.1.2 Euro-American T2 RD724 0.54
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 0.6 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.53 pyrazinamide
embB 4249518 p.His1002Arg missense_variant 0.51 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.5 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.5 ethionamide, 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
gyrA 7539 p.Thr80Ala missense_variant 0.54
gyrA 7585 p.Ser95Thr missense_variant 0.59
gyrA 9304 p.Gly668Asp missense_variant 0.53
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoC 763444 c.75T>C synonymous_variant 0.47
rpoC 764810 p.Pro481Thr missense_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.59
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.52
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.44
PPE35 2170692 c.-80T>G upstream_gene_variant 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Leu missense_variant 0.52
Rv2752c 3065920 p.Pro91Leu missense_variant 0.56
fbiD 3339040 c.-78T>C upstream_gene_variant 0.47
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.48
fbiB 3642874 p.Leu447Arg missense_variant 0.52
rpoA 3877967 p.Thr181Ala missense_variant 0.49
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.53
embB 4246584 p.Arg24Pro missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.44