TB-Profiler result

Run: SRR6785459
Summary

Run ID: SRR6785459

Sample name:

Date: 04-04-2023 15:57:27

Number of reads: 1299667

Percentage reads mapped: 99.37

Strain: lineage4.3.3

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
lineage4.3.3 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
tlyA 1918592 c.656delG frameshift_variant 0.12 capreomycin
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
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 1303095 c.165G>A synonymous_variant 1.0
Rv1258c 1407518 c.-178C>G upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472107 n.262A>C non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102713 c.330C>A synonymous_variant 0.22
katG 2156088 c.24T>A synonymous_variant 0.22
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2169063 p.Met517Lys missense_variant 0.5
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
Rv2752c 3064756 p.Val479Gly missense_variant 0.29
thyX 3067486 p.Phe154Ile missense_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087823 p.Ser335* stop_gained 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474717 c.711C>T synonymous_variant 0.15
fprA 3475037 p.Val344Ala missense_variant 0.14
Rv3236c 3613010 p.Tyr36Phe missense_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4040605 p.Leu34Ile missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244505 p.Gly425Trp missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0