TB-Profiler result

Run: SRR4033844

Summary

Run ID: SRR4033844

Sample name:

Date: 04-04-2023 06:22:33

Number of reads: 808331

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

Drug-resistance: Other


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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
ethA 4327068 c.405dupT frameshift_variant 0.14 ethionamide
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 1.0
gyrB 6065 p.Val276Met missense_variant 0.11
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
rpoB 759662 c.-145C>T upstream_gene_variant 0.12
rpoC 763082 c.-288C>T upstream_gene_variant 0.11
rpoC 764300 p.Gly311Cys missense_variant 0.15
rpoC 764879 p.Leu504Met missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765680 p.Asn771Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775809 p.Thr891Asn missense_variant 0.1
mmpL5 778129 p.Ala118Thr missense_variant 0.13
mmpS5 778744 p.Lys54Asn missense_variant 0.12
mmpR5 779000 p.Asn4Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.12
embR 1417449 c.-102C>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474228 n.572delA non_coding_transcript_exon_variant 0.12
rrl 1475729 n.2072C>A non_coding_transcript_exon_variant 0.12
rrl 1476493 n.2836A>T non_coding_transcript_exon_variant 0.12
fabG1 1673314 c.-126G>A upstream_gene_variant 0.14
inhA 1674952 p.Pro251Ala missense_variant 0.29
rpsA 1833995 c.454C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102156 p.Glu296Gly missense_variant 0.12
ndh 2102559 p.Ser162Gly missense_variant 0.13
ndh 2103131 c.-89C>A upstream_gene_variant 0.12
PPE35 2167900 p.Gly905Arg missense_variant 0.11
PPE35 2168057 p.Gln852His missense_variant 0.11
PPE35 2168463 p.Pro717His missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715348 c.-16G>A upstream_gene_variant 0.15
ahpC 2726279 c.87G>A synonymous_variant 0.14
ahpC 2726449 p.Ser86Leu missense_variant 0.14
ribD 2986945 p.Asp36Val missense_variant 0.11
Rv2752c 3065997 c.195C>T synonymous_variant 0.15
thyA 3073806 c.666C>G synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473942 c.-65C>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474235 p.Arg77Ser missense_variant 0.22
fprA 3474719 p.Ala238Val missense_variant 0.18
fbiB 3641898 p.Pro122Ser missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040892 c.-188A>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326475 c.999G>A synonymous_variant 0.12
ethA 4327722 c.-249C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0