TB-Profiler result

Run: SRR16149152
Summary

Run ID: SRR16149152

Sample name:

Date: 03-04-2023 16:29:21

Number of reads: 515277

Percentage reads mapped: 99.21

Strain: lineage4.2.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.1 Euro-American LAM7-TUR None 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val 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 6844 c.-458T>A upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 760131 p.Val109Phe missense_variant 0.15
rpoB 762291 p.Thr829Ala missense_variant 0.13
rpoC 763459 p.Lys30Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781814 c.255C>T synonymous_variant 0.17
embR 1417122 p.Val76Met missense_variant 0.17
atpE 1461125 c.81T>C synonymous_variant 0.25
atpE 1461255 p.Met71Val missense_variant 0.17
atpE 1461261 p.Leu73Met missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.25
rrl 1474266 n.609T>A non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102726 p.His106Arg missense_variant 1.0
katG 2155348 p.Met255Thr missense_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.3
PPE35 2167967 c.2646A>C synonymous_variant 0.27
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065193 c.999C>T synonymous_variant 0.18
Rv2752c 3066090 c.101delT frameshift_variant 0.15
Rv2752c 3066198 c.-8delG upstream_gene_variant 0.12
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612897 p.Gly74Cys missense_variant 0.13
fbiB 3641810 c.276G>C synonymous_variant 0.13
rpoA 3877956 p.Glu184Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247864 p.Ala451Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0