TB-Profiler result

Run: SRR2100832
Summary

Run ID: SRR2100832

Sample name:

Date: 03-04-2023 23:19:16

Number of reads: 2397116

Percentage reads mapped: 99.57

Strain: lineage4.6.2.2

Drug-resistance: HR-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
lineage4.6 Euro-American T;LAM None 0.97
lineage4.6.2 Euro-American T;LAM RD726 0.98
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407851 c.351delG frameshift_variant 0.97 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673393 c.-809G>C upstream_gene_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.36
folC 2746320 p.Pro427Ala missense_variant 0.94
thyA 3073806 c.666C>G synonymous_variant 0.28
fbiD 3339153 p.Leu12Phe missense_variant 0.25
Rv3083 3448567 p.His22Asp missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987011 c.168C>T synonymous_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 0.87
ethR 4326739 c.-810G>C upstream_gene_variant 0.95
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0