TB-Profiler result

Run: SRR22528530
Summary

Run ID: SRR22528530

Sample name:

Date: 04-04-2023 04:18:04

Number of reads: 1308759

Percentage reads mapped: 99.65

Strain: lineage4.4.1.1;lineage4.1.2.1

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 0.75
lineage4.4 Euro-American S;T None 0.24
lineage4.1.2 Euro-American T;H None 0.75
lineage4.4.1 Euro-American (S-type) S;T None 0.31
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.71
lineage4.4.1.1 Euro-American S;Orphans None 0.24
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 0.28 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid
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 8116 p.Thr272Ile missense_variant 0.39
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.91
mshA 575679 p.Asn111Ser missense_variant 0.8
rpoB 760115 c.309C>T synonymous_variant 0.64
rpoB 761528 p.Asp574Glu missense_variant 0.38
rpoC 765150 p.Gly594Glu missense_variant 0.7
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 1472687 n.842A>G non_coding_transcript_exon_variant 0.4
rrs 1473197 n.1352A>G non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.31
PPE35 2169840 p.Gly258Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.72
kasA 2518306 c.192C>A synonymous_variant 0.14
thyA 3074495 c.-24C>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.37
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.36
rpoA 3878630 c.-123G>C upstream_gene_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.58
embA 4244970 c.1738C>T synonymous_variant 0.23
embB 4248437 p.Thr642Ala missense_variant 0.14
ethR 4326703 c.-846T>C upstream_gene_variant 0.12
whiB6 4338514 p.Tyr3Cys missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408157 p.Leu16Val missense_variant 0.31