TB-Profiler result

Run: SRR10869004
Summary

Run ID: SRR10869004

Sample name:

Date: 02-04-2023 19:35:36

Number of reads: 1926481

Percentage reads mapped: 99.52

Strain: lineage4.3.4.2.1;lineage4.1.1.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.59
lineage4.1 Euro-American T;X;H None 0.45
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.45
lineage4.3.4 Euro-American (LAM) LAM RD174 0.59
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.43
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.59
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.58
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 761109 p.Asp435Tyr missense_variant 0.4 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.33 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
gyrB 6140 p.Val301Leu missense_variant 0.56
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.58
rpoC 765150 p.Gly594Glu missense_variant 0.36
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 1472998 n.1153C>T non_coding_transcript_exon_variant 0.57
inhA 1673474 c.-728C>G upstream_gene_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.54
alr 3840719 c.702A>G synonymous_variant 0.55
rpoA 3878619 c.-112A>C upstream_gene_variant 0.12
rpoA 3878630 c.-123G>C upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.43
embB 4249408 c.2895G>A synonymous_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.51
gid 4408156 p.Leu16Arg missense_variant 0.74