TB-Profiler result

Run: ERR2679274

Summary

Run ID: ERR2679274

Sample name:

Date: 31-03-2023 23:00:55

Number of reads: 472869

Percentage reads mapped: 99.61

Strain: lineage2.2.1

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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620667 p.Trp259Cys missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781518 c.-42G>T upstream_gene_variant 0.11
rpsL 781520 c.-40_-39insAAACAGAACGTG upstream_gene_variant 0.94
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473686 n.29T>A non_coding_transcript_exon_variant 0.22
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
PPE35 2167706 c.2907T>A synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168474 c.2139C>T synonymous_variant 0.14
PPE35 2170066 p.Ala183Thr missense_variant 0.15
PPE35 2170561 p.Gly18Arg missense_variant 0.15
PPE35 2170623 c.-11G>A upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289472 c.-231G>A upstream_gene_variant 0.13
kasA 2518655 p.Ala181Thr missense_variant 0.13
kasA 2519014 c.900G>A synonymous_variant 0.12
Rv2752c 3064589 p.Arg535Gly missense_variant 0.11
thyA 3074173 p.Ser100Leu missense_variant 0.14
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
Rv3236c 3613161 c.-45A>G upstream_gene_variant 0.11
fbiB 3641109 c.-426C>A upstream_gene_variant 1.0
panD 4044192 c.90C>T synonymous_variant 0.12
embC 4241554 c.1692G>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242793 c.-440A>T upstream_gene_variant 0.12
embA 4243367 p.Trp45Cys missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg 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
gid 4408214 c.-12G>A upstream_gene_variant 0.12
gid 4408277 c.-75T>C upstream_gene_variant 0.11