TB-Profiler result

Run: ERR4812966
Summary

Run ID: ERR4812966

Sample name:

Date: 01-04-2023 12:26:56

Number of reads: 643492

Percentage reads mapped: 99.52

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrB 5246 p.Ala3Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576123 p.Leu259Arg missense_variant 0.33
rpoC 764840 p.Ile491Val missense_variant 1.0
rpoC 764993 p.Ala542Ser missense_variant 0.11
rpoC 766137 p.Arg923Gln missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776751 p.Phe577Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801283 c.475C>A synonymous_variant 0.14
Rv1258c 1407188 c.153C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834894 c.1353C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288916 p.Val109Gly missense_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ribD 2987231 c.393G>A synonymous_variant 0.11
Rv2752c 3067017 c.-826G>T upstream_gene_variant 0.29
thyX 3067243 p.Leu235Met missense_variant 0.18
thyX 3067792 p.Pro52Ser missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449977 p.His492Asn missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474446 p.Gly147Val missense_variant 0.12
fprA 3474912 c.906G>T synonymous_variant 0.25
Rv3236c 3612632 p.Met162Thr missense_variant 0.12
fbiB 3641764 p.Leu77Arg missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040298 p.Gln136Arg missense_variant 0.11
embC 4239887 p.Arg9Ser missense_variant 0.17
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243112 p.Gly1084Trp missense_variant 0.12
embA 4243204 c.-28delT upstream_gene_variant 1.0
embB 4246277 c.-237G>A upstream_gene_variant 0.13
aftB 4268867 c.-31G>T upstream_gene_variant 0.2
ubiA 4269686 p.Glu50Lys missense_variant 0.14
ubiA 4269856 c.-23G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0