TB-Profiler result

Run: SRR14801488
Summary

Run ID: SRR14801488

Sample name:

Date: 03-04-2023 11:49:47

Number of reads: 1716530

Percentage reads mapped: 99.66

Strain: lineage4.8;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.58
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.43
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.63
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.4
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 4327333 c.140delT frameshift_variant 0.47 ethionamide, ethionamide
gid 4408115 c.87delC frameshift_variant 0.61 streptomycin
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 0.42
gyrA 9304 p.Gly668Asp missense_variant 0.46
fgd1 491742 c.960T>C synonymous_variant 0.46
mshA 575907 p.Ala187Val missense_variant 0.44
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576482 p.Val379Leu missense_variant 0.28
ccsA 620625 p.Ile245Met missense_variant 0.42
rpoC 763031 c.-339T>C upstream_gene_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776182 p.Asp767Asn missense_variant 0.46
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.39
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.59
rpsA 1834177 c.636A>C synonymous_variant 0.39
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.56
PPE35 2167926 p.Leu896Ser missense_variant 0.4
PPE35 2168149 p.Pro822Ser missense_variant 0.49
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725921 c.-272A>T upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 0.4
fbiD 3339734 p.Ala206Gly missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.34
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.45
embA 4244904 p.Val558Leu missense_variant 0.38
embB 4246584 p.Arg24Pro missense_variant 0.6
embB 4248319 c.1806A>T synonymous_variant 0.22
embB 4248933 p.Asn807Thr missense_variant 0.54
aftB 4267647 p.Asp397Gly missense_variant 0.3
ethR 4327084 c.-465G>A upstream_gene_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.42
gid 4407927 p.Glu92Asp missense_variant 0.37