TB-Profiler result

Run: ERR3509870
Summary

Run ID: ERR3509870

Sample name:

Date: 01-04-2023 02:32:54

Number of reads: 309700

Percentage reads mapped: 99.61

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 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.38 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 1.0 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
gyrB 6142 c.903G>T synonymous_variant 0.12
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 491379 c.597C>T synonymous_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.43
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763500 c.132delC frameshift_variant 0.12
rpoC 765687 p.Ala773Glu missense_variant 0.13
rpoC 766780 p.Glu1137Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775678 p.Lys935Glu missense_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778621 c.-141G>A upstream_gene_variant 0.2
mmpR5 779350 p.Gly121Trp missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304006 p.Pro359Gln missense_variant 0.14
Rv1258c 1406607 p.Val245Ala missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407097 p.Ser82Thr missense_variant 0.17
embR 1416397 p.Asp317Glu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674109 p.Leu224Met missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102686 c.357G>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169559 p.Phe352Leu missense_variant 0.12
PPE35 2170516 p.Gly33Arg missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288784 p.Thr153Ile missense_variant 1.0
pncA 2289745 c.-504C>T upstream_gene_variant 0.4
eis 2714169 c.1164G>T synonymous_variant 0.12
eis 2714191 p.Gln381Leu missense_variant 0.13
eis 2715470 c.-138G>T upstream_gene_variant 0.1
folC 2746787 p.Ala271Gly missense_variant 0.14
pepQ 2860615 c.-197T>C upstream_gene_variant 0.22
thyX 3067381 p.Tyr189His missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641974 p.Val147Asp missense_variant 0.17
fbiB 3642205 p.Asp224Gly missense_variant 1.0
fbiB 3642789 p.Glu419* stop_gained 0.13
alr 3840415 p.Pro336Thr missense_variant 0.17
rpoA 3878231 p.Val93Ile missense_variant 0.11
clpC1 4040070 p.Pro212Leu missense_variant 0.11
clpC1 4040130 p.Gly192Val missense_variant 0.11
embC 4239715 c.-148G>A upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244276 c.1044A>G synonymous_variant 0.15
embA 4245142 p.Ile637Thr missense_variant 0.12
embA 4245934 p.Pro901Arg missense_variant 0.12
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247108 p.Gly199Arg missense_variant 0.15
embB 4248422 p.Ala637Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
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