TB-Profiler result

Run: ERR9993151
Summary

Run ID: ERR9993151

Sample name:

Date: 02-04-2023 14:05:56

Number of reads: 2982153

Percentage reads mapped: 76.67

Strain: lineage4.4.1.1

Drug-resistance: Pre-XDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
embB 4248003 p.Gln497Arg 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
gyrB 6144 p.His302Arg missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576111 p.Ala255Gly missense_variant 0.21
rpoC 766485 p.Val1039Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779459 p.Tyr157Ser 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 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.13
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.16
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.17
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.13
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.11
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.14
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.13
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.13
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.13
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.13
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.13
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.13
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.13
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.13
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.13
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.13
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.12
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2156117 c.-6A>G upstream_gene_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086635 c.-185_-184insA upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0