TB-Profiler result

Run: SRR6982290
Summary

Run ID: SRR6982290

Sample name:

Date: 04-04-2023 18:33:04

Number of reads: 706555

Percentage reads mapped: 99.65

Strain: lineage4.3.2.1

Drug-resistance: HR-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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2154138 c.1973delT frameshift_variant 0.1 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 5520 p.Pro94Leu missense_variant 0.98
gyrB 5773 c.534T>C synonymous_variant 0.11
gyrB 6071 p.Phe278Leu missense_variant 0.14
gyrB 6217 c.978G>T synonymous_variant 0.1
gyrB 7058 p.Ile607Phe missense_variant 0.11
gyrB 7093 c.1856delA frameshift_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9410 p.Met703Ile missense_variant 0.11
mshA 575262 c.-85delC upstream_gene_variant 0.18
ccsA 619831 c.-60T>G upstream_gene_variant 0.26
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776265 p.Lys739Arg missense_variant 0.1
mmpR5 779123 p.Val45Ala missense_variant 0.18
mmpR5 779173 p.Ala62Thr missense_variant 0.12
mmpS5 779540 c.-635A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406353 p.Pro330Ser missense_variant 0.12
atpE 1461039 c.-6A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1476100 n.2443A>G non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102976 p.Gly23Trp missense_variant 0.18
PPE35 2170497 p.Ala39Val missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715145 p.Leu63Arg missense_variant 0.12
ahpC 2726071 c.-122C>T upstream_gene_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.22
folC 2746783 c.816C>T synonymous_variant 0.12
folC 2747701 c.-103T>C upstream_gene_variant 0.12
pepQ 2859462 c.957C>T synonymous_variant 0.2
ribD 2986941 p.Pro35Thr missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074533 c.-62G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568479 c.201T>C synonymous_variant 0.12
whiB7 3568779 c.-100T>C upstream_gene_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044201 c.81C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244831 p.Phe533Leu missense_variant 0.25
aftB 4267527 p.Ala437Asp missense_variant 0.12
aftB 4268795 c.42C>G synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0