TB-Profiler result

Run: ERR10748114
Summary

Run ID: ERR10748114

Sample name:

Date: 31-03-2023 10:44:44

Number of reads: 1537807

Percentage reads mapped: 99.92

Strain: lineage4.8.1;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 0.3
lineage4 Euro-American LAM;T;S;X;H None 0.72
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.25
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.72
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.27
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.73
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 7582 p.Asp94Gly missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.24 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 0.42 pyrazinamide
pncA 2288943 p.Thr100Ile missense_variant 0.4 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.28 ethambutol
ethA 4327347 p.Gly43Cys missense_variant 0.34 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 7114 c.-188C>G upstream_gene_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.37
gyrA 9304 p.Gly668Asp missense_variant 0.51
fgd1 491328 c.546C>G synonymous_variant 0.37
fgd1 491330 p.Lys183Met missense_variant 0.36
fgd1 491742 c.960T>C synonymous_variant 0.3
mshA 575907 p.Ala187Val missense_variant 0.28
ccsA 620625 p.Ile245Met missense_variant 0.39
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
rpoC 764822 p.Asp485Tyr missense_variant 0.23
mmpL5 775592 c.2889G>A synonymous_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.28
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.64
rpsA 1834177 c.636A>C synonymous_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 0.26
PPE35 2168149 p.Pro822Ser missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.32
fbiD 3339040 c.-78T>C upstream_gene_variant 0.59
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.15
Rv3083 3449315 p.Trp271* stop_gained 1.0
Rv3083 3449590 p.Ala363Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.21
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35
fbiB 3642874 p.Leu447Arg missense_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.25
embB 4247717 p.Leu402Val missense_variant 0.37
aftB 4267647 p.Asp397Gly missense_variant 0.14
whiB6 4338365 p.Cys53Arg missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.31
gid 4407927 p.Glu92Asp missense_variant 0.37