TB-Profiler result

Run: ERR9993034
Summary

Run ID: ERR9993034

Sample name:

Date: 02-04-2023 14:00:35

Number of reads: 3352794

Percentage reads mapped: 80.31

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu 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
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.31
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779302 p.Arg105Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406813 c.528T>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.27
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.27
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.27
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.3
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.27
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.27
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.27
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.27
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.26
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.26
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.27
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.28
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.28
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.1
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.1
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.12
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.13
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.26
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.24
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472670 n.824_825insTGG non_coding_transcript_exon_variant 0.18
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.16
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.16
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.12
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.17
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.18
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.15
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.16
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.16
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.17
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.16
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.16
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.16
rrs 1473002 n.1157G>C non_coding_transcript_exon_variant 0.16
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.16
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.17
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.17
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 1.0
rpoA 3878614 c.-107A>C upstream_gene_variant 0.2
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247738 p.Ala409Pro missense_variant 1.0
ethA 4326842 p.Tyr211Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0