TB-Profiler result

Run: ERR4800625
Summary

Run ID: ERR4800625

Sample name:

Date: 01-04-2023 09:57:21

Number of reads: 3028299

Percentage reads mapped: 99.61

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.98
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 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.97 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326767 c.706delA frameshift_variant 0.98 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 5332 c.93C>T synonymous_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8168 p.Glu289Asp missense_variant 0.98
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576482 p.Val379Leu missense_variant 0.17
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 0.99
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1673406 c.-796C>G upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.23
clpC1 4039729 p.Asp326Asn missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245417 p.Gly729Arg missense_variant 0.96
embB 4246584 p.Arg24Pro missense_variant 0.2
ubiA 4269296 p.Met180Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0