TB-Profiler result

Run: SRR3085281
Summary

Run ID: SRR3085281

Sample name:

Date: 04-04-2023 04:57:42

Number of reads: 2407953

Percentage reads mapped: 96.84

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 0.33 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.62 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
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 0.89 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 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
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 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416909 p.Gly147Trp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrl 1474828 n.1172delC non_coding_transcript_exon_variant 0.23
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.13
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834818 p.Lys426Arg missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.27
katG 2153970 p.Asp714Glu missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169581 c.1032C>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170147 p.Ser156Ala missense_variant 0.22
PPE35 2170550 c.63C>G synonymous_variant 0.11
PPE35 2170551 c.61delT frameshift_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746198 c.1401C>A synonymous_variant 0.13
Rv2752c 3064722 c.1470A>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
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
fbiB 3642187 p.Arg218Leu missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.13
clpC1 4039714 p.Tyr331His missense_variant 0.1
clpC1 4040057 c.648C>T synonymous_variant 0.13
clpC1 4040087 c.618G>T synonymous_variant 0.13
clpC1 4040090 c.615T>C synonymous_variant 0.13
clpC1 4040093 c.612C>G synonymous_variant 0.14
embC 4240011 p.Leu50Pro missense_variant 0.12
embC 4242217 c.2355C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4247090 p.Thr193Ala missense_variant 0.14
embB 4247098 c.585C>G synonymous_variant 0.12
embB 4247117 p.Val202Ile missense_variant 0.11
embB 4247516 p.Asn335Asp missense_variant 0.11
aftB 4267200 p.Trp546Leu missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267935 p.Val301Ala missense_variant 0.14
aftB 4268890 c.-54C>T upstream_gene_variant 0.13
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