TB-Profiler result

Run: ERR5865200
Summary

Run ID: ERR5865200

Sample name:

Date: 01-04-2023 23:51:42

Number of reads: 1131200

Percentage reads mapped: 99.73

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 761086 p.Thr427Ser missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288778 p.Val155Ala missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 6162 c.924delC frameshift_variant 0.25
gyrB 6268 c.1029C>A synonymous_variant 0.11
gyrB 6297 p.Gly353Val missense_variant 0.1
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 576751 p.Lys468Asn missense_variant 0.2
rpoC 762611 c.-759C>T upstream_gene_variant 0.2
rpoB 763059 p.Ile1085Phe missense_variant 0.17
rpoC 763728 p.Leu120Pro missense_variant 0.13
rpoC 764968 c.1599T>C synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.94
fbiC 1305183 p.Leu751Phe missense_variant 0.12
atpE 1461231 p.Ala63Ser missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673400 c.-40C>T upstream_gene_variant 0.11
rpsA 1833764 p.Asp75Asn missense_variant 0.13
rpsA 1834025 p.Gln162Lys missense_variant 0.11
rpsA 1834088 p.Val183Met missense_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 1.0
rpsA 1834942 p.Asp467Glu missense_variant 0.18
tlyA 1917785 c.-154delG upstream_gene_variant 0.12
tlyA 1917795 c.-145G>C upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102098 c.945G>A synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2167837 p.Gly926Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290044 c.-803G>T upstream_gene_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519143 c.1029G>C synonymous_variant 0.17
eis 2714319 c.1014G>A synonymous_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.18
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2746658 p.Gly314Val missense_variant 0.22
folC 2747135 p.Leu155His missense_variant 0.15
Rv2752c 3064916 p.Gly426Cys missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074036 p.Cys146Arg missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612046 c.1071G>A synonymous_variant 0.11
Rv3236c 3612839 p.Ala93Val missense_variant 0.17
rpoA 3878367 c.141C>T synonymous_variant 0.15
rpoA 3878487 c.21C>A synonymous_variant 0.13
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4040339 c.365delA frameshift_variant 0.12
panD 4044373 c.-92C>A upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268311 p.Ala176Thr missense_variant 0.11
ethA 4326266 p.Cys403Phe missense_variant 1.0
ethA 4326537 p.Val313Leu missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407952 p.Pro84Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0