TB-Profiler result

Run: SRR1184002
Summary

Run ID: SRR1184002

Sample name:

Date: 03-04-2023 05:20:10

Number of reads: 6185775

Percentage reads mapped: 99.44

Strain: lineage4.1.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.2 Euro-American (X-type) X1 None 0.98
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.Asp94Gly missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>C upstream_gene_variant 0.98 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
gid 4407835 c.366_367delCT 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
mshA 576057 c.711_712dupGG frameshift_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155296 c.816C>T synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339688 p.Thr191Pro missense_variant 0.18
Rv3083 3449787 c.1284C>T synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039676 c.1029G>A synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243833 p.Ala201Thr missense_variant 1.0
embB 4246930 p.Gln139His missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0