TB-Profiler result

Run: ERR1035295
Summary

Run ID: ERR1035295

Sample name:

Date: 31-03-2023 10:10:08

Number of reads: 10939324

Percentage reads mapped: 99.53

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 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 761155 p.Ser450Leu missense_variant 0.99 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2155102 p.Tyr337Cys missense_variant 0.14 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.99 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
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 0.99
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781365 c.-195T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305014 p.Thr695Lys missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.31
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.26
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.29
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.28
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.18
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.2
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.24
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.27
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.27
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.25
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.24
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.18
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.19
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.2
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.21
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.26
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.33
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.26
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.29
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.31
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.13
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.21
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.21
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.24
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.11
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.12
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.1
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.11
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.11
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.24
PPE35 2169866 c.747G>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407977 p.Gly76Cys missense_variant 0.99