TB-Profiler result

Run: ERR137194
Summary

Run ID: ERR137194

Sample name:

Date: 31-03-2023 13:57:40

Number of reads: 8978743

Percentage reads mapped: 99.65

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: HR-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
lineage2 East-Asian Beijing RD105 0.36
lineage4 Euro-American LAM;T;S;X;H None 0.64
lineage4.1 Euro-American T;X;H None 0.63
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.38
lineage4.1.2 Euro-American T;H None 0.61
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.36
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.63
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
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid
pncA 2289222 p.Val7Gly missense_variant 0.41 pyrazinamide
ethA 4326707 p.Trp256* stop_gained 0.31 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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9532 p.Gly744Ala missense_variant 0.62
fgd1 491591 p.Lys270Met missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 0.37
mshA 575679 p.Asn111Ser missense_variant 0.65
mshA 575907 p.Ala187Val missense_variant 0.41
mshA 576328 c.981T>C synonymous_variant 0.6
ccsA 620625 p.Ile245Met missense_variant 0.41
rpoB 760115 c.309C>T synonymous_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.29
rpoC 764617 c.1248C>T synonymous_variant 0.32
rpoC 765150 p.Gly594Glu missense_variant 0.61
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.4
mmpL5 776182 p.Asp767Asn missense_variant 0.41
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36
Rv1258c 1407079 c.261delC frameshift_variant 0.65
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.39
PPE35 2169320 p.Leu431Phe missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.63
ahpC 2726327 c.135C>A synonymous_variant 0.61
ribD 2987307 p.Ala157Pro missense_variant 0.21
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086731 c.-89A>G upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449925 c.1422C>T synonymous_variant 0.64
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.37
clpC1 4038857 c.1848C>A synonymous_variant 0.25
embC 4242425 p.Arg855Gly missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.66
embA 4243346 c.114A>G synonymous_variant 0.37
embA 4243460 c.228C>T synonymous_variant 0.36
embA 4243969 p.Val246Gly missense_variant 0.61
aftB 4267647 p.Asp397Gly missense_variant 0.32
whiB6 4338371 p.Thr51Pro missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.39
gid 4407927 p.Glu92Asp missense_variant 0.32