TB-Profiler result

Run: SRR998802
Summary

Run ID: SRR998802

Sample name:

Date: 04-04-2023 23:36:59

Number of reads: 3567260

Percentage reads mapped: 99.35

Strain: lineage5.1.1;lineage4.1.3

Drug-resistance: MDR-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 0.94
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.09
lineage4.1 Euro-American T;X;H None 0.89
lineage5.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.1
lineage4.1.3 Euro-American T;X;H None 0.87
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 0.06
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
rpoB 761139 p.His445Asp missense_variant 0.95 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.92 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid
pncA 2288844 p.Ile133Thr missense_variant 0.93 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.89 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.87 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 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 0.97
rpoC 763904 p.Ala179Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.94
fbiC 1302899 c.-32A>G upstream_gene_variant 0.16
fbiC 1304610 c.1680C>T synonymous_variant 0.85
Rv1258c 1406740 p.His201Tyr missense_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.17
ndh 2103112 c.-70G>T upstream_gene_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715511 c.-179C>T upstream_gene_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 0.92
ald 3087084 c.266delA frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840932 c.489C>T synonymous_variant 0.12
rpoA 3878493 c.15G>A synonymous_variant 0.14
ddn 3986987 c.144G>T synonymous_variant 0.14
ddn 3987180 p.Asp113Asn missense_variant 0.15
clpC1 4040010 p.Ala232Asp missense_variant 0.12
embC 4240986 p.Arg375Gln missense_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.87
embA 4244220 c.988C>T synonymous_variant 0.13
embA 4244635 p.Val468Ala missense_variant 0.12
embA 4245147 p.Pro639Ser missense_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 0.1
ethR 4326928 c.-621G>A upstream_gene_variant 0.15
ethA 4327103 p.Gly124Asp missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17