TB-Profiler result

Run: ERR4827764
Summary

Run ID: ERR4827764

Sample name:

Date: 01-04-2023 18:18:42

Number of reads: 2094702

Percentage reads mapped: 99.68

Strain: lineage4.8;lineage2

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
lineage2 East-Asian Beijing RD105 0.05
lineage4 Euro-American LAM;T;S;X;H None 0.96
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.93
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 761161 p.Leu452Pro missense_variant 0.18 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.16 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
gyrA 9226 p.Ser642Phe missense_variant 0.87
fgd1 491046 p.Gln88His missense_variant 0.94
mshA 576108 p.Ala254Gly missense_variant 0.3
rpoC 766645 p.Glu1092Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.13
mmpL5 776182 p.Asp767Asn missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.15
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 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.9
PPE35 2170623 c.-11G>A upstream_gene_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746448 p.Asp384Ala missense_variant 0.1
fbiD 3339734 p.Ala206Gly missense_variant 0.28
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.3
rpoA 3878641 c.-134C>G upstream_gene_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.19
embB 4246584 p.Arg24Pro missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.1
gid 4407927 p.Glu92Asp missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0