TB-Profiler result

Run: SRR5341253
Summary

Run ID: SRR5341253

Sample name:

Date: 04-04-2023 10:11:23

Number of reads: 1069636

Percentage reads mapped: 99.45

Strain: lineage4.2

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
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
pncA 2288778 p.Val155Gly missense_variant 1.0 pyrazinamide
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
gyrA 7585 p.Ser95Thr missense_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 762066 p.Arg754Cys missense_variant 0.1
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472145 n.300_301insT non_coding_transcript_exon_variant 0.22
rrl 1475518 n.1861A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518197 p.Asp28Ala missense_variant 0.13
kasA 2518200 p.Ile29Asn missense_variant 0.14
kasA 2518218 p.Gly35Ala missense_variant 0.11
kasA 2518226 p.Ala38Ser missense_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067251 p.Val232Ala missense_variant 0.14
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.11
embB 4249653 c.3141delC frameshift_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0