TB-Profiler result

Run: ERR2512378
Summary

Run ID: ERR2512378

Sample name:

Date: 31-03-2023 19:00:01

Number of reads: 2708449

Percentage reads mapped: 99.32

Strain: lineage3.1.1

Drug-resistance: Sensitive

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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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
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 9270 p.Asp657Tyr missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576111 p.Ala255Gly missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.97
rpoC 762740 c.-630G>A upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763633 c.264T>G synonymous_variant 0.12
rpoC 764131 c.762T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
fbiC 1304652 c.1722C>T synonymous_variant 0.12
Rv1258c 1406327 c.1014G>T synonymous_variant 0.14
Rv1258c 1406357 c.984C>A synonymous_variant 0.14
Rv1258c 1406386 p.Ala319Thr missense_variant 0.15
Rv1258c 1406523 p.Val273Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472533 n.688T>A non_coding_transcript_exon_variant 0.4
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.29
rrl 1473920 n.263G>T non_coding_transcript_exon_variant 0.5
rrl 1474423 n.766G>A non_coding_transcript_exon_variant 0.18
rrl 1476244 n.2587G>T non_coding_transcript_exon_variant 0.14
inhA 1674860 c.662delG frameshift_variant 0.12
rpsA 1834883 p.Gln448Lys missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102351 p.Arg231Leu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167719 p.Ser965Ile missense_variant 0.13
PPE35 2167745 p.Thr956Arg missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169577 p.Asn346Asp missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289041 c.201G>A synonymous_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448889 p.Arg129Leu missense_variant 0.24
Rv3083 3449133 c.630G>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612286 c.830delG frameshift_variant 0.18
Rv3236c 3612383 p.Phe245Ser missense_variant 0.13
rpoA 3877766 p.Ala248Ser missense_variant 0.13
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
aftB 4268619 p.Val73Gly missense_variant 0.21
aftB 4268808 p.Val10Ala missense_variant 0.12
aftB 4268913 c.-77A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0