TB-Profiler result

Run: ERR4831557

Summary

Run ID: ERR4831557

Sample name:

Date: 01-04-2023 21:00:39

Number of reads: 1794862

Percentage reads mapped: 98.81

Strain: lineage4.3.2.1;lineage4.1.1.3

Drug-resistance: Pre-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.45
lineage4.1 Euro-American T;X;H None 0.55
lineage4.3.2 Euro-American (LAM) LAM3 None 0.45
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.59
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.58
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.43
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 0.55 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.63 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin
katG 2155167 p.Ser315Thr missense_variant 0.47 isoniazid
pncA 2288827 p.Val139Met missense_variant 0.54 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.51 isoniazid
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol
ethA 4326876 c.597delC frameshift_variant 0.48 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 5520 p.Pro94Leu missense_variant 0.47
gyrB 6608 p.Val457Leu missense_variant 0.54
gyrA 7222 c.-80C>T upstream_gene_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 0.43
rpoC 765150 p.Gly594Glu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801354 c.546G>A synonymous_variant 0.51
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.47
tlyA 1917972 c.33A>G synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 0.51
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877949 p.Thr187Ala missense_variant 0.52
clpC1 4038287 c.2418C>T synonymous_variant 0.45
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.51
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4249408 c.2895G>A synonymous_variant 0.57
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.37