TB-Profiler result

Run: ERR11082159
Summary

Run ID: ERR11082159

Sample name:

Date: 10-04-2023 03:17:34

Number of reads: 4298785

Percentage reads mapped: 99.63

Strain: lineage4.8;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 0.5
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.51
lineage4.1.2 Euro-American T;H None 0.49
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.49
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 761076 p.Phe424Val missense_variant 0.46 rifampicin
rpoB 761095 p.Leu430Pro missense_variant 0.44 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.55 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid
embB 4247429 p.Met306Val missense_variant 0.53 ethambutol
ethA 4326160 p.Tyr438* stop_gained 0.47 ethionamide
gid 4407988 c.200_214delATATCGGTAGCGGAG disruptive_inframe_deletion 0.39 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 0.51
gyrA 9304 p.Gly668Asp missense_variant 0.54
fgd1 491591 p.Lys270Met missense_variant 0.5
mshA 575679 p.Asn111Ser missense_variant 0.61
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 759627 c.-180A>C upstream_gene_variant 0.43
rpoB 760115 c.309C>T synonymous_variant 0.43
rpoC 765150 p.Gly594Glu missense_variant 0.47
rpoC 766744 p.Gln1125His missense_variant 0.5
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154799 p.Trp438Leu missense_variant 0.44
PPE35 2169503 c.1109delG frameshift_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289109 p.Val45Met missense_variant 0.5
kasA 2518076 c.-39C>T upstream_gene_variant 0.39
Rv2752c 3067180 c.-989C>A upstream_gene_variant 0.51
ald 3086788 c.-32T>C upstream_gene_variant 0.51
fbiD 3339324 c.207G>T synonymous_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.42
embA 4243228 c.-5G>A upstream_gene_variant 0.51
embB 4246584 p.Arg24Pro missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0