TB-Profiler result

Run: ERR4827429
Summary

Run ID: ERR4827429

Sample name:

Date: 01-04-2023 18:02:30

Number of reads: 1131429

Percentage reads mapped: 99.53

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 0.99
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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 762300 p.Lys832Glu missense_variant 1.0
rpoC 766255 c.2886G>T synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406150 c.1191G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
fabG1 1673560 p.Lys41Gln missense_variant 0.1
inhA 1674135 c.-67C>T upstream_gene_variant 1.0
inhA 1674279 c.78A>G synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101740 p.Gln435* stop_gained 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168863 c.1750C>T synonymous_variant 1.0
PPE35 2168981 c.1632A>T synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860200 c.219G>A synonymous_variant 0.12
Rv2752c 3067190 c.-999C>A upstream_gene_variant 1.0
fbiD 3339691 p.Pro192Thr missense_variant 0.15
clpC1 4040242 p.Thr155Ser missense_variant 0.12
clpC1 4040250 p.Glu152Gly missense_variant 0.12
embC 4240596 p.Leu245Arg missense_variant 0.11
embC 4240599 p.Val246Ala missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.1
embA 4244391 c.1159C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4247395 c.882C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0