TB-Profiler result

Run: ERR3994117
Summary

Run ID: ERR3994117

Sample name:

Date: 01-04-2023 03:42:46

Number of reads: 717209

Percentage reads mapped: 99.97

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
ethA 4326261 c.1212delC frameshift_variant 0.11 ethionamide
ethA 4326707 p.Trp256* stop_gained 0.2 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
gyrB 5761 p.Trp174Cys missense_variant 0.17
gyrB 6139 c.900G>C synonymous_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491210 p.Trp143Leu missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575850 p.Arg168His missense_variant 0.33
rpoB 759803 c.-4C>T upstream_gene_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760591 p.Val262Asp missense_variant 0.13
rpoC 763851 p.Ala161Asp missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775716 p.Arg922Leu missense_variant 0.2
mmpL5 776041 p.Ala814Ser missense_variant 0.18
mmpL5 776074 p.Val803Ile missense_variant 0.13
mmpL5 776257 p.Ala742Ser missense_variant 0.2
mmpR5 779020 p.Gly11Ser missense_variant 0.14
mmpR5 779098 p.Gly37Cys missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 1.0
rplC 801154 p.Gly116Cys missense_variant 0.17
fbiC 1305356 p.Gly809Asp missense_variant 0.2
Rv1258c 1406304 p.Gly346Ala missense_variant 0.29
embR 1417056 p.Pro98Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674094 p.Gly219Trp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101995 p.Glu350* stop_gained 0.13
katG 2155023 c.1089C>A synonymous_variant 0.12
katG 2156271 c.-160G>A upstream_gene_variant 0.17
PPE35 2168763 p.Thr617Lys missense_variant 0.23
PPE35 2169051 p.Asn521Ser missense_variant 0.17
PPE35 2169337 p.Asp426Tyr missense_variant 0.2
PPE35 2169896 c.717C>T synonymous_variant 0.13
PPE35 2170740 c.-128T>A upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288985 p.Asp86Gly missense_variant 0.17
pncA 2289565 c.-324G>T upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726147 c.-46A>G upstream_gene_variant 0.12
ahpC 2726638 p.Ala149Gly missense_variant 0.13
Rv2752c 3064867 p.Val442Ala missense_variant 0.12
Rv2752c 3065259 c.933G>A synonymous_variant 0.11
Rv2752c 3065493 c.699G>T synonymous_variant 0.12
thyX 3067563 p.Leu128Pro missense_variant 0.15
thyA 3073927 p.Ala182Val missense_variant 0.17
thyA 3074139 p.Gln111His missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474036 c.30C>G synonymous_variant 0.18
fprA 3474714 p.Glu236Asp missense_variant 0.11
fprA 3475221 c.1217_1218delTG frameshift_variant 0.14
fprA 3475228 p.Asp408His missense_variant 0.13
ddn 3986854 p.Ser4* stop_gained 0.11
clpC1 4038319 p.Pro796Ala missense_variant 0.18
clpC1 4038361 p.Glu782* stop_gained 0.17
clpC1 4039219 p.Val496Leu missense_variant 0.25
clpC1 4039400 c.1305G>A synonymous_variant 0.22
embC 4240274 p.Pro138Thr missense_variant 0.22
embC 4241656 c.1794G>A synonymous_variant 0.13
embC 4242208 c.2346T>A synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242984 p.Arg1041His missense_variant 0.18
embA 4244547 p.Ile439Phe missense_variant 0.4
embA 4246462 p.Gly1077Asp missense_variant 0.15
embB 4248041 p.Ala510Thr missense_variant 0.2
embB 4249195 c.2682C>A synonymous_variant 0.25
ethA 4327413 p.Trp21Arg missense_variant 0.2
ethA 4327863 c.-390G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0