TB-Profiler result

Run: SRR998698
Summary

Run ID: SRR998698

Sample name:

Date: 04-04-2023 23:32:10

Number of reads: 1126024

Percentage reads mapped: 92.96

Strain: lineage4.6.2.2;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 1.0
lineage4.6 Euro-American T;LAM None 0.72
lineage4.1 Euro-American T;X;H None 0.31
lineage4.1.3 Euro-American T;X;H None 0.23
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.69
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 0.23 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.3 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
pncA 2288844 p.Ile133Thr missense_variant 0.28 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.18 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.29 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
gyrA 9557 c.2256G>C synonymous_variant 0.24
mshA 575313 c.-35C>G upstream_gene_variant 0.4
rpoB 762244 c.2444_2446dupTGC disruptive_inframe_insertion 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.33
fbiC 1304610 c.1680C>T synonymous_variant 0.39
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917894 c.-46_-45insTGT upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.58
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715511 c.-179C>T upstream_gene_variant 0.29
thyX 3067238 c.708C>T synonymous_variant 0.17
thyX 3067474 p.Pro158Ala missense_variant 0.67
thyX 3067772 c.174C>T synonymous_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.26
Rv3083 3448567 p.His22Asp missense_variant 0.77
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 0.73
rpoA 3878641 c.-135delG upstream_gene_variant 0.12
embC 4240986 p.Arg375Gln missense_variant 0.22
embC 4242220 c.2361_2376delCAACGGCATTCCCGCC frameshift_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.4
aftB 4267272 p.Lys522Arg missense_variant 0.45
ethR 4326739 c.-810G>C upstream_gene_variant 0.69
ethA 4328004 c.-531C>T upstream_gene_variant 0.78
whiB6 4338595 c.-75delG upstream_gene_variant 1.0