TB-Profiler result

Run: SRR9971319

Summary

Run ID: SRR9971319

Sample name:

Date: 04-04-2023 23:22:20

Number of reads: 3640957

Percentage reads mapped: 95.23

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288731 p.Ala171Thr missense_variant 1.0 pyrazinamide
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
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoC 764817 p.Val483Gly missense_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775967 p.Met838Ile missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>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 0.14
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.14
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.13
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
ethA 4327439 p.Ala12Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0