TB-Profiler result

Run: ERR4423629
Summary

Run ID: ERR4423629

Sample name:

Date: 01-04-2023 05:55:59

Number of reads: 1484783

Percentage reads mapped: 91.73

Strain: lineage3

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 0.99
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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155700 p.Asn138His missense_variant 0.97 isoniazid
embB 4249518 p.His1002Arg missense_variant 1.0 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 7965 c.667dupG frameshift_variant 0.2
gyrA 8343 p.Ile348Val missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.78
rpoB 759746 c.-61C>T upstream_gene_variant 0.93
rpoB 761006 c.1200C>T synonymous_variant 0.2
rpoB 761292 p.Val496Met missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764789 p.Arg474Cys missense_variant 0.2
rpoC 765119 p.Gly584Trp missense_variant 0.17
rpoC 766903 c.3534C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776351 c.2130G>C synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304886 p.Trp652* stop_gained 0.18
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 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.94
ahpC 2726117 c.-76T>A upstream_gene_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4239967 c.105G>T synonymous_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0