TB-Profiler result

Run: ERR7764394
Summary

Run ID: ERR7764394

Sample name:

Date: 02-04-2023 05:46:08

Number of reads: 1192196

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: Other

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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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
ethA 4326267 p.Cys403Gly missense_variant 1.0 ethionamide
ethA 4326488 p.Ser329Leu missense_variant 1.0 ethionamide
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
fgd1 490742 c.-41C>T upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777072 p.Lys470Met 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 2168406 p.Leu736Gln missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860051 p.Arg123Gln missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ribD 2987506 p.Leu223Arg missense_variant 0.22
fbiD 3339734 p.Ala206Gly missense_variant 0.4
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474052 p.Phe16Val missense_variant 0.25
clpC1 4038632 c.2073G>A synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.15
embC 4240427 p.Ser189Cys missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.36
embB 4246584 p.Arg24Pro missense_variant 0.38
embB 4247015 p.Ser168Ala missense_variant 0.45
embB 4247028 p.Leu172Arg missense_variant 0.75
embB 4247033 p.Ser174Arg missense_variant 0.57
ethA 4328025 c.-552T>A upstream_gene_variant 0.16
whiB6 4338200 p.Asp108His missense_variant 0.19
whiB6 4338440 c.81dupT frameshift_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