TB-Profiler result

Run: ERR4799370
Summary

Run ID: ERR4799370

Sample name:

Date: 01-04-2023 09:03:54

Number of reads: 2611033

Percentage reads mapped: 99.66

Strain: lineage4.8;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 0.36
lineage4 Euro-American LAM;T;S;X;H None 0.6
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.37
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.63
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.37
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 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.33 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid
katG 2155322 p.Ala264Thr missense_variant 0.67 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.37 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.32 ethambutol
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 0.37
gyrA 9304 p.Gly668Asp missense_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 0.41
ccsA 620625 p.Ile245Met missense_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.43
rpoC 766488 p.Pro1040Arg missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.44
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4
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 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.37
PPE35 2167926 p.Leu896Ser missense_variant 0.3
PPE35 2168149 p.Pro822Ser missense_variant 0.65
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.36
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 0.33
clpC1 4039729 p.Asp326Asn missense_variant 0.65
embC 4240061 p.Phe67Val missense_variant 0.56
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 0.4
ethA 4326676 p.Ser266Arg missense_variant 0.23
ethA 4327065 p.Cys137Arg missense_variant 0.17
ethA 4327436 p.Gly13Val missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407925 p.Pro93Leu missense_variant 0.62
gid 4407927 p.Glu92Asp missense_variant 0.4