TB-Profiler result

Run: ERR4817460
Summary

Run ID: ERR4817460

Sample name:

Date: 01-04-2023 15:00:17

Number of reads: 466009

Percentage reads mapped: 99.65

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
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 7179 p.Leu647Ser missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761061 p.Ala419Thr missense_variant 0.2
rpoB 761341 p.Lys512Arg missense_variant 0.14
rpoB 762653 p.Trp949Cys missense_variant 0.13
rpoB 762847 p.Pro1014Arg missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778928 c.-448T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801380 p.Val191Glu missense_variant 0.18
fbiC 1305135 c.2205C>A synonymous_variant 0.1
embR 1417140 p.Ala70Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
tlyA 1917785 c.-155C>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155525 p.Val196Asp missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289945 c.-704T>A upstream_gene_variant 0.22
folC 2747022 p.Val193Ile missense_variant 1.0
folC 2747025 p.Ala192Thr missense_variant 0.22
pepQ 2859501 c.918G>A synonymous_variant 0.17
pepQ 2859769 p.Phe217Ser missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339512 p.Ala132Glu missense_variant 0.11
Rv3083 3448821 c.318C>T synonymous_variant 0.67
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474676 p.Val224Met missense_variant 0.14
fprA 3475279 p.Val425Met missense_variant 0.25
whiB7 3568648 p.Pro11His missense_variant 0.2
fbiA 3641164 p.Ile208Val missense_variant 1.0
fbiB 3642335 p.Ser267Arg missense_variant 0.12
alr 3840894 p.Leu176Pro missense_variant 0.15
rpoA 3877774 p.Ala245Glu missense_variant 0.11
rpoA 3878393 p.Arg39Ser missense_variant 0.18
rpoA 3878429 p.Glu27* stop_gained 0.17
ddn 3986821 c.-23C>T upstream_gene_variant 0.12
clpC1 4039328 c.1377A>T synonymous_variant 0.22
embC 4241656 c.1794G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244239 p.Trp336Ser missense_variant 0.22
aftB 4268649 p.Trp63* stop_gained 0.22
ubiA 4268996 p.Arg280Cys missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0