TB-Profiler result

Run: ERR9029917
Summary

Run ID: ERR9029917

Sample name:

Date: 02-04-2023 09:23:51

Number of reads: 6741557

Percentage reads mapped: 99.59

Strain: lineage4.7;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.66
lineage4 Euro-American LAM;T;S;X;H None 0.36
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.68
lineage4.7 Euro-American (mainly T) T1;T5 None 0.34
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.69
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 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.63 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.65 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.7 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 0.74 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.62 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.66 ethambutol
ethA 4326305 p.Ser390Phe missense_variant 0.72 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 0.78
gyrA 9304 p.Gly668Asp missense_variant 0.68
fgd1 491742 c.960T>C synonymous_variant 0.72
mshA 575907 p.Ala187Val missense_variant 0.63
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 0.64
rpoC 763031 c.-339T>C upstream_gene_variant 0.69
rpoC 764817 p.Val483Ala missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.66
mmpL5 776182 p.Asp767Asn missense_variant 0.65
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303897 c.967C>T synonymous_variant 0.61
Rv1258c 1406760 c.580_581insC frameshift_variant 0.64
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.28
rpsA 1834177 c.636A>C synonymous_variant 0.69
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.61
PPE35 2167926 p.Leu896Ser missense_variant 0.8
PPE35 2169261 p.Leu451Arg missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747740 c.-142A>G upstream_gene_variant 0.33
thyA 3074003 p.Gly157Ser missense_variant 0.36
ald 3086788 c.-32T>C upstream_gene_variant 0.76
ald 3087208 p.Leu130Pro missense_variant 0.61
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.61
Rv3236c 3612424 c.693G>A synonymous_variant 0.35
Rv3236c 3612813 p.Thr102Ala missense_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.64
embB 4249732 c.3219C>G synonymous_variant 0.43
aftB 4267647 p.Asp397Gly missense_variant 0.64
whiB6 4338473 c.49A>C synonymous_variant 0.63
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.73
gid 4407927 p.Glu92Asp missense_variant 0.71
gid 4408413 c.-211C>T upstream_gene_variant 0.7