TB-Profiler result

Run: ERR4407453
Summary

Run ID: ERR4407453

Sample name:

Date: 01-04-2023 05:44:39

Number of reads: 468457

Percentage reads mapped: 78.28

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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 2155179 p.Asp311Glu missense_variant 0.14 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 7728 p.Arg143Gly missense_variant 0.1
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.11
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 766337 p.Asp990Asn missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779295 c.-815A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304070 c.1140C>G synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472965 n.1120C>G non_coding_transcript_exon_variant 0.14
rrl 1474403 n.746G>A non_coding_transcript_exon_variant 0.13
rrl 1474586 n.929T>C non_coding_transcript_exon_variant 0.12
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.14
rrl 1475499 n.1842C>A non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168591 c.2022G>A synonymous_variant 0.12
PPE35 2168600 c.2013G>A synonymous_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169293 c.1320T>C synonymous_variant 0.22
PPE35 2169308 c.1305C>T synonymous_variant 0.22
PPE35 2169322 c.1291T>C synonymous_variant 0.15
PPE35 2169323 c.1290C>G synonymous_variant 0.15
PPE35 2169326 c.1287C>T synonymous_variant 0.15
PPE35 2169337 p.Asp426His missense_variant 0.15
Rv1979c 2221822 p.Ser448Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.2
kasA 2518609 p.Met165Ile missense_variant 0.2
kasA 2519345 p.Leu411Phe missense_variant 0.25
pepQ 2859827 p.Ala198Thr missense_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
panD 4043924 p.Asp120Asn missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245880 p.Asp883Gly missense_variant 0.1
embA 4246485 c.3255_3257delTCG disruptive_inframe_deletion 0.13
embB 4249790 p.Lys1093Glu missense_variant 0.1
aftB 4268598 c.238delG frameshift_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0