TB-Profiler result

Run: ERR4818346
Summary

Run ID: ERR4818346

Sample name:

Date: 01-04-2023 15:30:30

Number of reads: 1095108

Percentage reads mapped: 99.1

Strain: lineage4.1.1.3.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 0.99
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.93 ethambutol
gid 4408100 c.102delG frameshift_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
rpoC 765084 p.Arg572His missense_variant 0.19
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765920 p.Ile851Val missense_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775883 p.Ile866Leu missense_variant 0.12
mmpL5 775918 p.Val855Ile missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.25
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.25
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.25
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.25
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.25
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.14
Rv2752c 3067066 c.-876delG upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.12
fprA 3474165 c.159C>G synonymous_variant 0.1
clpC1 4039829 p.Leu292Phe missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethR 4327309 c.-240G>C upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0