TB-Profiler result

Run: ERR4815552
Summary

Run ID: ERR4815552

Sample name:

Date: 01-04-2023 13:55:42

Number of reads: 520004

Percentage reads mapped: 99.55

Strain: lineage2.2.1.1

Drug-resistance: HR-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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7067 p.Tyr610His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7845 p.Ala182Ser missense_variant 0.15
gyrA 8870 c.1569G>C synonymous_variant 0.17
gyrA 8897 c.1596T>C synonymous_variant 0.12
gyrA 8915 c.1614A>G synonymous_variant 0.12
gyrA 8924 c.1623C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490891 p.Val37Ile missense_variant 0.29
fgd1 491499 c.717G>C synonymous_variant 0.2
fgd1 491611 p.Ile277Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760241 c.435G>C synonymous_variant 0.25
rpoB 760597 p.Thr264Ile missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765478 c.2109T>G synonymous_variant 0.17
rpoC 766690 c.3321G>T synonymous_variant 0.11
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 777215 c.1266C>T synonymous_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781501 c.-59C>T upstream_gene_variant 0.25
rpsL 781637 c.78C>T synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406998 p.Ala115Thr missense_variant 0.2
Rv1258c 1407395 c.-55G>T upstream_gene_variant 0.2
embR 1416322 p.Asn342Lys missense_variant 1.0
embR 1416517 c.831C>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473804 n.147T>C non_coding_transcript_exon_variant 0.17
inhA 1674016 c.-186G>A upstream_gene_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156513 c.-402A>T upstream_gene_variant 0.17
PPE35 2167899 p.Gly905Val missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170624 c.-12A>G upstream_gene_variant 0.13
Rv1979c 2223026 p.Ala47Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518815 p.Arg234Leu missense_variant 0.17
kasA 2519320 p.Phe402Leu missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715026 p.Glu103Lys missense_variant 0.25
eis 2715511 c.-179C>T upstream_gene_variant 0.11
folC 2746897 c.702C>T synonymous_variant 0.25
folC 2747631 c.-33C>A upstream_gene_variant 0.17
Rv2752c 3066271 c.-80A>G upstream_gene_variant 0.22
thyA 3074371 p.Met34Lys missense_variant 0.25
thyA 3074612 c.-141G>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087693 p.Asp292Asn missense_variant 0.14
Rv3083 3449198 p.Arg232His missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.93
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641178 c.-357G>T upstream_gene_variant 0.25
fbiB 3642282 p.Glu250Lys missense_variant 0.22
clpC1 4040604 p.Leu34Pro missense_variant 0.14
clpC1 4040803 c.-99G>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243608 p.Ala126Thr missense_variant 0.11
embB 4246763 p.Pro84Ala missense_variant 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248840 p.Pro776His missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326698 p.Arg259His missense_variant 0.18
whiB6 4338310 p.Gly71Asp missense_variant 0.11
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
gid 4408029 c.174C>T synonymous_variant 0.22