TB-Profiler result

Run: ERR2653098
Summary

Run ID: ERR2653098

Sample name:

Date: 31-03-2023 22:31:11

Number of reads: 679108

Percentage reads mapped: 99.47

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 None 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
gyrB 6620 p.Asp461His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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 5338 c.99C>T synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 1.0
mmpL5 778033 p.Gln150* stop_gained 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289070 p.Phe58Val missense_variant 1.0
ald 3087854 c.1035G>A synonymous_variant 0.11
alr 3841071 p.Gly117Asp missense_variant 1.0
clpC1 4040525 c.180C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Thr missense_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407590 p.Ala205Thr missense_variant 1.0