TB-Profiler result

Run: ERR4799994
Summary

Run ID: ERR4799994

Sample name:

Date: 01-04-2023 09:31:35

Number of reads: 4595950

Percentage reads mapped: 99.58

Strain: lineage4.3.3;lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 0.39
lineage4 Euro-American LAM;T;S;X;H None 0.57
lineage4.3 Euro-American (LAM) mainly-LAM None 0.55
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.35
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.41
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.54
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 7581 p.Asp94Asn missense_variant 0.39 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.44 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.49 isoniazid
pncA 2288720 c.521_522insT frameshift_variant 0.43 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.4 ethambutol
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 8040 p.Gly247Ser missense_variant 0.54
gyrA 9304 p.Gly668Asp missense_variant 0.99
gyrA 9758 c.2457C>T synonymous_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 0.55
ccsA 620079 c.189C>T synonymous_variant 0.37
rpoB 759746 c.-61C>T upstream_gene_variant 0.44
rpoC 762434 c.-936T>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.35
rpoC 764995 c.1626C>G synonymous_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.63
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.41
katG 2154724 p.Arg463Leu missense_variant 0.41
katG 2156196 c.-85C>T upstream_gene_variant 0.55
PPE35 2167926 p.Leu896Ser missense_variant 0.48
PPE35 2168604 p.Pro670Leu missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.38
pncA 2289365 c.-125delC upstream_gene_variant 0.43
kasA 2518919 p.Gly269Ser missense_variant 0.67
ahpC 2726105 c.-88G>A upstream_gene_variant 0.54
folC 2746340 p.Ala420Val missense_variant 0.58
thyA 3073868 p.Thr202Ala missense_variant 0.58
thyA 3074247 p.His75Gln missense_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 0.46
clpC1 4038287 c.2418C>T synonymous_variant 0.47
clpC1 4040675 c.30C>G synonymous_variant 0.37
embC 4242075 p.Arg738Gln missense_variant 0.49
embA 4242643 c.-590C>T upstream_gene_variant 0.99
ethA 4327229 p.Leu82Arg missense_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.42
gid 4408156 p.Leu16Arg missense_variant 0.54