TB-Profiler result

Run: ERR552812

Summary

Run ID: ERR552812

Sample name:

Date: 19-10-2023 14:53:50

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage2.2.1;lineage1.2.1.2.1

Drug-resistance: Other


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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 0.65
lineage1 Indo-Oceanic EAI RD239 0.34
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.67
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.64
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.34
lineage1.2.1.2 Indo-Oceanic NA RD239 0.36
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.33
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
gid 4408100 c.102delG frameshift_variant 0.33 streptomycin
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 6112 p.Met291Ile missense_variant 0.37
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.37
gyrA 9143 c.1842T>C synonymous_variant 0.38
gyrA 9260 c.1959G>C synonymous_variant 0.41
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 0.62
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.4
rpoC 763884 p.Ala172Val missense_variant 0.31
rpoC 763886 c.517C>A synonymous_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 0.32
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67
embR 1417019 p.Cys110Tyr missense_variant 0.44
atpE 1460907 c.-138T>C upstream_gene_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.3
inhA 1674162 c.-40C>T upstream_gene_variant 0.38
rpsA 1834177 c.636A>C synonymous_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.33
kasA 2519048 p.Gly312Ser missense_variant 0.35
ahpC 2726051 c.-142G>A upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.34
Rv3083 3448714 p.Asp71His missense_variant 0.34
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.36
fprA 3475159 p.Asn385Asp missense_variant 0.38
whiB7 3568488 c.191delG frameshift_variant 0.41
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65
fbiB 3640557 c.-978T>C upstream_gene_variant 0.3
clpC1 4040517 p.Val63Ala missense_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 0.29
embC 4241042 p.Asn394Asp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.64
embA 4243580 c.348G>A synonymous_variant 0.4
embA 4244420 c.1188G>C synonymous_variant 0.35
embA 4245969 p.Pro913Ser missense_variant 0.34
embB 4247578 c.1065G>A synonymous_variant 0.39
embB 4247646 p.Glu378Ala missense_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.59
ubiA 4269387 p.Glu149Asp missense_variant 0.37
aftB 4269606 c.-770T>C upstream_gene_variant 0.41
ubiA 4269864 c.-32delG upstream_gene_variant 0.38
ethA 4326676 p.Ser266Arg missense_variant 0.68
whiB6 4338361 p.Arg54Gln missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.34
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.38
gid 4407927 p.Glu92Asp missense_variant 0.65