TB-Profiler result

Run: SRR1173213
Summary

Run ID: SRR1173213

Sample name:

Date: 03-04-2023 03:19:29

Number of reads: 4931826

Percentage reads mapped: 89.54

Strain: lineage4.1.1.3

Drug-resistance: Pre-XDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.99
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
gyrA 7581 p.Asp94Tyr missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.91 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.53 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.91 ethionamide
ethA 4326604 c.869dupA frameshift_variant 1.0 ethionamide, 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762284 c.2478G>T synonymous_variant 0.12
rpoB 762285 p.Arg827Cys missense_variant 0.88
rpoB 762293 c.2487T>G synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.11
rpoC 763717 c.348T>C synonymous_variant 0.11
rpoC 763723 c.354G>C synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.13
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.13
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.13
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.14
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.14
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.14
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.11
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.13
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.12
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.14
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G 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
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0