TB-Profiler result

Run: ERR4828788

Summary

Run ID: ERR4828788

Sample name:

Date: 01-04-2023 19:05:09

Number of reads: 1137132

Percentage reads mapped: 96.2

Strain: lineage4.1.2.1

Drug-resistance: 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
lineage4.1 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 1.0 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288806 p.Ala146Thr missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, ethionamide
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 6084 p.Gly282Asp missense_variant 0.12
gyrB 6207 p.Ala323Val missense_variant 0.11
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 575462 p.Ser39Thr missense_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759853 p.Ser16Asn missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760363 p.Asp186Gly missense_variant 0.12
rpoC 763794 p.Glu142Gly missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_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 1472902 n.1057C>A non_coding_transcript_exon_variant 0.29
rrs 1472932 n.1087C>T non_coding_transcript_exon_variant 0.17
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.18
rpsA 1833937 c.400_402dupGTC conservative_inframe_insertion 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221995 c.1170G>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714303 c.1029dupC frameshift_variant 1.0
ribD 2987555 c.717C>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568498 p.Glu61Gly missense_variant 0.1
alr 3840755 c.666C>T synonymous_variant 1.0
alr 3841362 p.Thr20Met missense_variant 1.0
embC 4239668 c.-195G>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268737 p.Val34Ile missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0