TB-Profiler result

Run: ERR4829931
Summary

Run ID: ERR4829931

Sample name:

Date: 01-04-2023 19:46:19

Number of reads: 829617

Percentage reads mapped: 99.61

Strain: lineage4.1.1.2;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 0.68
lineage4 Euro-American LAM;T;S;X;H None 0.35
lineage4.1 Euro-American T;X;H None 0.35
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.34
lineage4.1.1.2 Euro-American (X-type) X1 None 0.38
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 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.33 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.64 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.7 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.59 ethambutol
gid 4407851 c.351delG frameshift_variant 0.16 streptomycin
gid 4408087 c.115delC frameshift_variant 0.62 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 8741 c.1440C>A synonymous_variant 0.31
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.64
rpoB 759746 c.-61C>T upstream_gene_variant 0.68
rpoB 761052 p.Pro416Ala missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 0.68
rpoC 763031 c.-339T>C upstream_gene_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.45
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471673 n.-172delG upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.4
katG 2155296 c.816C>T synonymous_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.65
pncA 2289365 c.-125delC upstream_gene_variant 0.76
ahpC 2726105 c.-88G>A upstream_gene_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449787 c.1284C>T synonymous_variant 0.32
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.67
embC 4242075 p.Arg738Gln missense_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.42
embA 4243833 p.Ala201Thr missense_variant 0.39
embA 4244347 p.Trp372* stop_gained 0.12
embB 4246930 p.Gln139His missense_variant 0.5
embB 4249408 c.2895G>A synonymous_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.64