TB-Profiler result

Run: SRR12830400
Summary

Run ID: SRR12830400

Sample name:

Date: 03-04-2023 06:59:21

Number of reads: 405863

Percentage reads mapped: 99.81

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 2154463 p.Ala550Asp missense_variant 0.12 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 5149 c.-91G>T upstream_gene_variant 0.12
gyrB 5942 p.Glu235Lys missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8550 p.Ala417Ser missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490993 p.Gly71Cys missense_variant 0.12
ccsA 620364 c.474C>A synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303248 c.318G>A synonymous_variant 0.11
embR 1417533 c.-186C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474401 n.744C>A non_coding_transcript_exon_variant 0.25
rrl 1474511 n.854G>T non_coding_transcript_exon_variant 0.4
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
rrl 1475310 n.1653A>G non_coding_transcript_exon_variant 0.2
rrl 1475372 n.1715A>G non_coding_transcript_exon_variant 0.2
rrl 1476379 n.2722G>A non_coding_transcript_exon_variant 0.29
fabG1 1673690 p.Val84Glu missense_variant 0.12
inhA 1673716 c.-486G>A upstream_gene_variant 0.12
rpsA 1834382 p.Glu281* stop_gained 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 1.0
ndh 2102701 p.Ser114Arg missense_variant 0.13
ndh 2102782 c.261C>T synonymous_variant 0.15
katG 2154366 c.1746A>G synonymous_variant 0.12
katG 2154396 c.1716G>A synonymous_variant 0.13
PPE35 2169347 c.1266C>T synonymous_variant 0.14
PPE35 2169634 p.Ala327Ser missense_variant 0.12
Rv1979c 2222966 p.Thr67Ala missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289708 c.-467G>T upstream_gene_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726720 p.Cys176* stop_gained 0.15
Rv2752c 3065982 c.210G>T synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087126 p.Cys103Arg missense_variant 0.12
Rv3083 3449854 p.Met451Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612313 p.Asp268Glu missense_variant 0.12
Rv3236c 3613029 c.88T>C synonymous_variant 0.12
Rv3236c 3613039 c.78A>G synonymous_variant 0.12
fbiA 3641461 p.Pro307Thr missense_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038858 p.Arg616Leu missense_variant 0.13
clpC1 4040515 p.Glu64* stop_gained 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246345 p.Arg1038Leu missense_variant 0.17
ethA 4326098 p.Gln459Arg missense_variant 0.12
ethR 4327354 c.-195G>T upstream_gene_variant 0.12
ethA 4327460 p.Leu5Pro missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 1.0