TB-Profiler result

Run: SRR6832792
Summary

Run ID: SRR6832792

Sample name:

Date: 04-04-2023 17:38:43

Number of reads: 1004642

Percentage reads mapped: 98.74

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 2155168 p.Ser315Thr missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7715 c.414G>C synonymous_variant 0.12
gyrA 8024 c.723T>A synonymous_variant 0.29
gyrA 8040 p.Gly247Ser missense_variant 0.75
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759793 c.-14T>A upstream_gene_variant 0.2
rpoC 764809 c.1440C>T synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777031 p.Ile484Val missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800904 c.96G>A synonymous_variant 0.12
atpE 1461071 c.27C>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472654 n.809G>A non_coding_transcript_exon_variant 0.17
rrl 1474050 n.393A>G non_coding_transcript_exon_variant 0.15
rrl 1476705 n.3048C>G non_coding_transcript_exon_variant 0.33
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673773 p.Asn112Asp missense_variant 0.2
fabG1 1674163 p.Gly242Ser missense_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155668 c.444G>A synonymous_variant 0.14
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156307 c.-196T>C upstream_gene_variant 0.12
PPE35 2169230 c.1383G>A synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726612 c.420C>T synonymous_variant 0.18
folC 2746340 p.Ala420Val missense_variant 1.0
Rv2752c 3065455 p.Gln246Arg missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568814 c.-135T>C upstream_gene_variant 0.2
rpoA 3878289 c.219C>T synonymous_variant 0.12
ddn 3987084 c.245_246delCG frameshift_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4040438 p.Glu89Asp missense_variant 0.15
embC 4241667 p.Ala602Glu missense_variant 0.14
embC 4242305 p.Ile815Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4246623 p.Gly37Val missense_variant 0.14
ethA 4328369 c.-896G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407977 p.Gly76Cys missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0