TB-Profiler result

Run: ERR4799983
Summary

Run ID: ERR4799983

Sample name:

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

Number of reads: 3383128

Percentage reads mapped: 99.43

Strain: lineage4;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 0.93
lineage4 Euro-American LAM;T;S;X;H None 0.05
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.34
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.31
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 7563 p.Gly88Cys missense_variant 0.64 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.75 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.74 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.68 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 0.59 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
pncA 2288746 c.495delC frameshift_variant 0.54 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.57 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 9304 p.Gly668Asp missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 0.94
rpoB 759746 c.-61C>T upstream_gene_variant 0.94
rpoC 762434 c.-936T>G upstream_gene_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.93
mmpR5 779236 p.Leu83Phe missense_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.9
PPE35 2168423 c.2190G>A synonymous_variant 0.19
PPE35 2168604 p.Pro670Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.94
pncA 2289365 c.-125delC upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 0.92
Rv2752c 3066376 c.-185C>T upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474718 p.Ala238Thr missense_variant 0.64
alr 3841473 c.-53G>A upstream_gene_variant 0.63
embC 4239887 p.Arg9Gly missense_variant 0.43
embC 4242075 p.Arg738Gln missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326446 p.Gly343Glu missense_variant 0.52
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407943 p.Gln87Arg missense_variant 0.38
gid 4408335 c.-133A>G upstream_gene_variant 0.54