TB-Profiler result

Run: ERR038747
Summary

Run ID: ERR038747

Sample name:

Date: 31-03-2023 08:41:40

Number of reads: 15070519

Percentage reads mapped: 99.6

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 761076 p.Phe424Val missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2154255 c.1856dupT frameshift_variant 1.0 isoniazid
pncA 2289043 p.Ser67Pro missense_variant 0.95 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326696 c.773_777dupGGCGC frameshift_variant 0.97 ethionamide
gid 4408115 c.87delC frameshift_variant 1.0 streptomycin
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 762276 p.Arg824Ser missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 767305 p.Tyr1312* stop_gained 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.27
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.23
eis 2715586 c.-254G>C upstream_gene_variant 0.41
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3064552 p.Arg547Pro missense_variant 0.25
Rv2752c 3064741 p.Gly484Ala missense_variant 0.26
Rv2752c 3066004 c.187delG frameshift_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.27
ald 3086767 c.-53A>C upstream_gene_variant 0.99
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642734 c.1200G>C synonymous_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4039932 p.Gly258Val missense_variant 0.3
embC 4239842 c.-21C>A upstream_gene_variant 0.19
embC 4242425 p.Arg855Gly missense_variant 0.22
embC 4242476 p.Pro872Ala missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.44
embC 4242827 p.Leu989Val missense_variant 0.2
aftB 4267715 c.1122G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.23
ethA 4327672 c.-199G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0