TB-Profiler result

Run: SRR10808922
Summary

Run ID: SRR10808922

Sample name:

Date: 02-04-2023 19:15:19

Number of reads: 3103464

Percentage reads mapped: 99.59

Strain: lineage4.4.2;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 0.8
lineage4 Euro-American LAM;T;S;X;H None 0.24
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.79
lineage4.4 Euro-American S;T None 0.2
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.4.2 Euro-American T1;T2 None 0.22
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
fabG1 1673423 c.-17G>T upstream_gene_variant 0.16 isoniazid, 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 7017 p.Ala593Val missense_variant 0.2
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 491742 c.960T>C synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.83
mshA 576108 p.Ala254Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.73
rpoC 763031 c.-339T>C upstream_gene_variant 0.74
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.81
mmpL5 776182 p.Asp767Asn missense_variant 0.73
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.82
PPE35 2168602 c.2010delC frameshift_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987049 p.Phe71Val missense_variant 0.79
Rv2752c 3066099 p.Met31Ile missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.74
embB 4246508 c.-6G>A upstream_gene_variant 0.24
embB 4249495 p.Phe994Leu missense_variant 0.84
aftB 4267647 p.Asp397Gly missense_variant 0.69
aftB 4268928 c.-92C>T upstream_gene_variant 0.17
aftB 4269375 c.-539G>A upstream_gene_variant 0.21
whiB6 4338594 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.78
gid 4407927 p.Glu92Asp missense_variant 0.87