TB-Profiler result

Run: ERR5866248
Summary

Run ID: ERR5866248

Sample name:

Date: 02-04-2023 00:35:12

Number of reads: 1188704

Percentage reads mapped: 99.74

Strain: lineage4.8

Drug-resistance: RR-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 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
rpoB 761109 p.Asp435Tyr missense_variant 0.94 rifampicin
pncA 2288959 c.282delC frameshift_variant 1.0 pyrazinamide
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 7017 p.Ala593Val missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407062 c.279G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154670 p.Ser481Trp missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747750 c.-152G>A upstream_gene_variant 1.0
Rv2752c 3064977 c.1215C>T synonymous_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243331 c.99G>T synonymous_variant 1.0
embB 4248444 p.Asn644Thr missense_variant 1.0
aftB 4267607 p.Glu410Asp missense_variant 0.11
ethA 4326906 p.Leu190Phe missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408059 p.His48Gln missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0