TB-Profiler result

Run: ERR2510682
Summary

Run ID: ERR2510682

Sample name:

Date: 31-03-2023 18:53:33

Number of reads: 2370531

Percentage reads mapped: 98.35

Strain: 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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 7572 p.Ser91Pro missense_variant 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.69 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155892 p.Asp74Tyr missense_variant 0.15 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.88 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619784 c.-107G>A upstream_gene_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.14
mmpL5 777262 p.Thr407Ala missense_variant 0.14
mmpL5 777263 c.1218G>C synonymous_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303965 c.1035G>A synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.12
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1474828 n.1172delC non_coding_transcript_exon_variant 0.12
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.26
rrl 1475175 n.1518G>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.12
ndh 2102604 c.439T>C synonymous_variant 0.13
ndh 2102610 c.433T>C synonymous_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.16
katG 2153970 p.Asp714Glu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.19
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.15
PPE35 2170147 p.Ser156Ala missense_variant 0.42
PPE35 2170157 p.Ala152Ser missense_variant 0.2
PPE35 2170308 p.Leu102Ala missense_variant 0.12
PPE35 2170313 c.300G>C synonymous_variant 0.11
PPE35 2170349 c.264C>A synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289361 c.-125delC upstream_gene_variant 0.12
folC 2746174 c.1425A>G synonymous_variant 0.12
ribD 2987211 p.Arg125Ser missense_variant 0.14
thyA 3074514 c.-43T>C upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
Rv3083 3449049 c.546C>G synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612965 p.Val51Glu missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.22
clpC1 4039714 p.Tyr331His missense_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.22
clpC1 4040057 c.648C>T synonymous_variant 0.23
clpC1 4040087 c.618G>T synonymous_variant 0.16
clpC1 4040090 c.615T>C synonymous_variant 0.16
clpC1 4040093 c.612C>G synonymous_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.14
embC 4240475 p.Ala205Thr missense_variant 0.14
embC 4242217 c.2355C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244247 p.Val339Ile missense_variant 0.12
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4247090 p.Thr193Ala missense_variant 0.14
embB 4247098 c.585C>G synonymous_variant 0.12
embB 4247512 c.999T>C synonymous_variant 0.12
embB 4247516 p.Asn335Asp missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267935 p.Val301Ala missense_variant 0.12
ethR 4327633 p.Ile29Phe missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0