TB-Profiler result

Run: SRR5153717

Summary

Run ID: SRR5153717

Sample name:

Date: 04-04-2023 09:23:37

Number of reads: 5415584

Percentage reads mapped: 97.47

Strain: lineage4.1.2.1

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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrB 6620 p.Asp461His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7510 p.His70Arg missense_variant 0.71 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761114 c.1312_1314delAAC conservative_inframe_deletion 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155222 p.Gly297Val missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
folC 2747151 p.Ser150Gly missense_variant 0.93 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu 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
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.18
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0