TB-Profiler result

Run: ERR11081829
Summary

Run ID: ERR11081829

Sample name:

Date: 09-04-2023 12:08:51

Number of reads: 1351495

Percentage reads mapped: 99.61

Strain: lineage4.8

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
lineage4.8 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 761101 p.Gln432Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288703 p.Val180Gly missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576373 c.1026G>T synonymous_variant 0.12
ccsA 620262 c.372C>T synonymous_variant 0.4
ccsA 620351 p.Arg154His missense_variant 0.4
rpoC 764817 p.Val483Gly missense_variant 1.0
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 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.11
kasA 2519143 c.1029G>C synonymous_variant 0.11
fbiD 3339576 c.459G>A synonymous_variant 0.13
fbiB 3640974 c.-561T>G upstream_gene_variant 1.0
rpoA 3878105 p.Glu135Lys missense_variant 0.17
clpC1 4038534 p.Arg724His missense_variant 0.17
panD 4044400 c.-119G>A upstream_gene_variant 0.17
embC 4241699 p.Met613Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243920 p.Gly230Ser missense_variant 0.12
embA 4245825 p.Asp865Asn missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.15
whiB6 4338234 c.288A>G synonymous_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