TB-Profiler result

Run: SRR15600351
Summary

Run ID: SRR15600351

Sample name:

Date: 03-04-2023 14:15:57

Number of reads: 1642911

Percentage reads mapped: 99.64

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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289194 c.47dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247469 p.Tyr319Ser 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
mshA 576108 p.Ala254Gly missense_variant 0.45
rpoC 763328 c.-42_-41insT upstream_gene_variant 1.0
rpoC 765710 p.Ala781Thr missense_variant 0.98
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
rrl 1473429 n.-229G>T upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.13
rrl 1476354 n.2699_2700delCT non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2703_2704insGC non_coding_transcript_exon_variant 0.12
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.15
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167880 c.2733C>T synonymous_variant 0.95
PPE35 2170048 p.Leu189Val missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087095 c.276C>T synonymous_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.44
ddn 3986911 p.Arg23Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0