TB-Profiler result

Run: ERR4812952
Summary

Run ID: ERR4812952

Sample name:

Date: 01-04-2023 12:26:29

Number of reads: 625463

Percentage reads mapped: 99.49

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-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 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7570 p.Ala90Val missense_variant 0.38 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.63 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288886 c.355dupT frameshift_variant 1.0 pyrazinamide, pyrazinamide
folC 2747454 p.Arg49Trp missense_variant 1.0 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
gid 4407985 p.Gly73Ala missense_variant 0.93 streptomycin
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 5612 p.Val125Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491521 c.739C>A synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576708 p.Arg454His missense_variant 0.11
ccsA 620441 p.Gly184Val missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760902 p.His366Asn missense_variant 0.1
rpoB 761401 p.Arg532Leu missense_variant 0.11
rpoC 765050 p.Ser561Pro missense_variant 0.92
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304196 c.1266C>T synonymous_variant 0.12
embR 1416890 p.Leu153Pro missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102181 p.Asp288Tyr missense_variant 0.18
Rv1979c 2222501 p.Ala222Thr missense_variant 1.0
Rv1979c 2222540 p.Gly209Cys missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
fprA 3474160 p.Gly52Trp missense_variant 0.11
whiB7 3568760 c.-81G>T upstream_gene_variant 0.15
fbiA 3640721 p.Pro60Leu missense_variant 0.14
alr 3840459 p.Ser321Trp missense_variant 0.11
alr 3840844 c.577C>T synonymous_variant 0.12
rpoA 3878609 c.-102T>A upstream_gene_variant 0.29
embC 4242341 p.Thr827Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243131 p.Pro1090Leu missense_variant 0.1
aftB 4267873 p.Gln322Glu missense_variant 1.0
aftB 4269723 c.-887G>T upstream_gene_variant 0.12
ethA 4326268 c.1206C>A synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0