TB-Profiler result

Run: ERR2515602
Summary

Run ID: ERR2515602

Sample name:

Date: 31-03-2023 21:01:08

Number of reads: 333834

Percentage reads mapped: 99.65

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 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
embB 4247609 p.Ser366Pro missense_variant 0.1 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 6214 c.975G>A synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9159 p.Ala620Ser missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491132 p.Gly117Val missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575576 p.Leu77Met missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620624 p.Ile245Thr missense_variant 0.12
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
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776883 p.Ile533Asn missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801128 p.Ala107Asp missense_variant 0.11
fbiC 1303057 c.128delA frameshift_variant 0.17
fbiC 1303255 p.Thr109Ala missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471679 n.-167C>A upstream_gene_variant 0.13
rrs 1472058 n.213T>C non_coding_transcript_exon_variant 1.0
rrs 1472699 n.854G>A non_coding_transcript_exon_variant 0.17
rrl 1473828 n.171G>A non_coding_transcript_exon_variant 0.11
inhA 1674144 c.-58G>T upstream_gene_variant 0.12
inhA 1674461 p.Lys87Arg missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834680 p.Met380Thr missense_variant 0.1
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
PPE35 2168119 p.Ser832Gly missense_variant 0.17
PPE35 2169196 p.Pro473Ala missense_variant 0.22
PPE35 2170437 p.Gly59Asp missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289264 c.-23T>C upstream_gene_variant 0.13
ahpC 2726430 p.Ala80Thr missense_variant 0.11
folC 2747602 c.-4T>C upstream_gene_variant 0.14
Rv2752c 3065806 p.Arg129His missense_variant 0.22
thyA 3073700 p.Lys258Glu missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449344 p.Val281Met missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474015 c.9C>A synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641024 p.Asp161Val missense_variant 0.12
fbiA 3641332 p.Gly264Arg missense_variant 0.94
fbiB 3641592 p.Leu20Val missense_variant 0.11
rpoA 3877686 c.822A>G synonymous_variant 0.1
rpoA 3877930 p.Ile193Ser missense_variant 0.14
clpC1 4038947 c.1758C>T synonymous_variant 0.1
embC 4240327 p.Leu155Phe missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267157 c.1680G>A synonymous_variant 0.15
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
gid 4408182 c.21G>A synonymous_variant 0.14
gid 4408413 c.-211C>A upstream_gene_variant 0.15