TB-Profiler result

Run: ERR7361964
Summary

Run ID: ERR7361964

Sample name:

Date: 02-04-2023 04:14:26

Number of reads: 1352140

Percentage reads mapped: 99.55

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575663 p.Gly106Trp missense_variant 0.22
ccsA 620075 p.Gly62Val missense_variant 0.25
rpoB 763123 p.Ile1106Thr missense_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473977 n.320G>T non_coding_transcript_exon_variant 0.15
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.17
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
fabG1 1673473 p.Pro12Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102510 p.Ala178Asp missense_variant 0.12
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290237 c.-996G>T upstream_gene_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746928 p.Pro224His missense_variant 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3067710 p.Ser79* stop_gained 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339384 c.267C>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.18
fprA 3475042 p.Gly346Cys missense_variant 0.15
fbiB 3642059 p.Asn175Lys missense_variant 0.11
fbiB 3642384 p.Leu284Val missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038802 p.Tyr635His missense_variant 0.12
clpC1 4039523 p.Phe394Leu missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.14
embC 4240252 c.390G>T synonymous_variant 0.12
embC 4241634 p.Gly591Val missense_variant 0.15
embC 4241664 p.Gly601Val missense_variant 0.25
embC 4242317 p.Glu819* stop_gained 0.25
embC 4242347 p.Ala829Ser missense_variant 0.4
embA 4242491 c.-742C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243961 c.729G>T synonymous_variant 0.13
embA 4246474 p.Val1081Ala missense_variant 0.15
embB 4246718 p.Ala69Pro missense_variant 0.12
embB 4249733 p.Pro1074Asn missense_variant 0.14
aftB 4267715 c.1122G>T synonymous_variant 0.23
ubiA 4269271 p.Val188Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0