TB-Profiler result

Run: ERR6326065
Summary

Run ID: ERR6326065

Sample name:

Date: 02-04-2023 01:58:20

Number of reads: 1993168

Percentage reads mapped: 98.46

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 761155 p.Ser450Leu missense_variant 0.98 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2288868 p.Val125Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247781 p.Met423Thr missense_variant 1.0 ethambutol
gid 4407965 p.Ala80Pro missense_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 6140 p.Val301Leu missense_variant 1.0
gyrB 6365 p.Gly376Cys missense_variant 0.18
gyrB 6429 p.Glu397Gly missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490655 c.-128T>C upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoC 763604 p.Gly79Ser missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.4
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.33
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.33
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.29
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.29
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.4
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.4
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.33
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.33
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.33
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.33
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.33
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.29
rrl 1473722 n.65G>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153952 p.Phe720Leu missense_variant 0.11
PPE35 2167890 p.Gly908Asp missense_variant 0.11
Rv1979c 2222427 p.Asp246Glu missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517954 c.-161G>A upstream_gene_variant 0.12
ahpC 2726557 p.Ala122Glu missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086868 p.Ala17Ser missense_variant 0.1
fbiD 3339734 p.Ala206Gly missense_variant 0.58
fbiD 3339746 p.Ala210Gly missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
whiB7 3568428 c.252A>C synonymous_variant 0.62
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040477 c.228G>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
embB 4248324 p.Ala604Gly missense_variant 0.33
ethA 4327301 p.Asp58Gly missense_variant 0.15
ethA 4328127 c.-654C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0