TB-Profiler result

Run: SRR7829595
Summary

Run ID: SRR7829595

Sample name:

Date: 04-04-2023 20:22:37

Number of reads: 1814508

Percentage reads mapped: 99.69

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 8434 p.Thr378Ile missense_variant 0.11
gyrA 8453 c.1152A>G synonymous_variant 0.14
gyrA 8667 p.Ala456Thr missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 p.Ala696Gly missense_variant 0.1
rpoC 764484 p.Arg372Gln missense_variant 0.12
rpoC 765235 c.1866C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776378 p.Phe701Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417527 c.-180A>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472415 n.570T>C non_coding_transcript_exon_variant 0.11
rrs 1472523 n.678A>G non_coding_transcript_exon_variant 0.1
rrl 1474643 n.986A>T non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
inhA 1674448 p.Gly83Arg missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.16
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.21
katG 2156463 c.-352G>A upstream_gene_variant 0.18
PPE35 2169840 p.Gly258Asp missense_variant 0.96
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289594 c.-393_-354delAGATGTACGAAACCGTCGTTGTATCAACGGTGGTAATGCA upstream_gene_variant 1.0
ahpC 2726090 c.-103C>T upstream_gene_variant 0.12
pepQ 2859801 c.618G>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244966 c.1734C>T synonymous_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246706 p.Gly65Ser missense_variant 0.12
embB 4247533 p.Met340Ile missense_variant 0.13
embB 4249645 c.3132G>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338609 c.-88T>G upstream_gene_variant 1.0
gid 4408093 p.Gly37Val missense_variant 1.0