TB-Profiler result

Run: SRR10380053
Summary

Run ID: SRR10380053

Sample name:

Date: 02-04-2023 17:25:14

Number of reads: 788269

Percentage reads mapped: 99.49

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 491247 c.465C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.36
mshA 576468 p.Val374Gly missense_variant 0.5
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoB 762310 p.His835Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778710 p.Tyr66His missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406614 p.Glu243* stop_gained 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.17
rrl 1474786 n.1129A>G non_coding_transcript_exon_variant 0.15
rrl 1476287 n.2630A>G non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103023 p.Pro7Arg missense_variant 0.1
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726234 p.Gln14His missense_variant 0.11
folC 2747127 p.Met158Val missense_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3449081 p.Val193Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878618 c.-111A>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243868 c.636G>T synonymous_variant 0.11
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0