TB-Profiler result

Run: ERR038742
Summary

Run ID: ERR038742

Sample name:

Date: 31-03-2023 08:41:06

Number of reads: 6121825

Percentage reads mapped: 99.59

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2154538 p.Gln525Pro missense_variant 0.99 isoniazid
pncA 2288757 p.Gly162Asp missense_variant 0.55 pyrazinamide
pncA 2288851 p.Val131Phe missense_variant 0.49 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248025 p.Glu504Asp 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 759939 p.Pro45Ser missense_variant 0.26
rpoB 760975 p.Met390Thr missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.36
rpoC 765920 p.Ile851Val missense_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.3
rrl 1475090 n.1433A>C non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.29
eis 2715586 c.-254G>C upstream_gene_variant 0.43
thyA 3073806 c.666C>G synonymous_variant 0.32
ald 3086767 c.-53A>C upstream_gene_variant 1.0
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
fbiB 3641955 p.Gly141Arg missense_variant 0.23
fbiB 3642734 c.1200G>C synonymous_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.23
clpC1 4039932 p.Gly258Val missense_variant 0.22
embC 4239842 c.-21C>A upstream_gene_variant 0.19
embC 4242476 p.Pro872Ala missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.34
aftB 4267715 c.1122G>A synonymous_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4327672 c.-199G>A upstream_gene_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0