TB-Profiler result

Run: ERR2516647
Summary

Run ID: ERR2516647

Sample name:

Date: 31-03-2023 21:39:15

Number of reads: 1129554

Percentage reads mapped: 99.62

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
gyrB 6742 p.Glu501Asp missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
gid 4408022 c.180delA frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765590 p.Arg741Ser missense_variant 1.0
rpoC 766485 p.Val1039Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.17
fabG1 1673412 c.-28G>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155029 c.1083C>T synonymous_variant 0.13
PPE35 2168007 p.Ile869Thr missense_variant 0.2
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2221887 c.1278T>G synonymous_variant 0.22
Rv1979c 2223123 c.42G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715340 c.-8C>T upstream_gene_variant 0.92
ahpC 2725949 c.-244G>A upstream_gene_variant 0.12
ribD 2987307 p.Ala157Pro missense_variant 0.14
Rv2752c 3064688 p.Lys502Glu missense_variant 0.12
Rv2752c 3064771 p.Ala474Val missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.22
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
fprA 3474645 c.639C>A synonymous_variant 0.14
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612410 p.Leu236Pro missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326330 p.Tyr382His missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0