TB-Profiler result

Run: ERR4796473
Summary

Run ID: ERR4796473

Sample name:

Date: 01-04-2023 06:52:44

Number of reads: 4102435

Percentage reads mapped: 99.58

Strain: lineage3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
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
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247495 p.Asp328Tyr missense_variant 1.0 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 6963 p.Arg575His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576113 p.Arg256Gly missense_variant 0.27
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762418 p.Arg871Leu missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
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 776181 p.Asp767Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473863 n.206A>T non_coding_transcript_exon_variant 0.14
rrl 1474949 n.1292G>T non_coding_transcript_exon_variant 0.22
rrl 1475533 n.1876A>T non_coding_transcript_exon_variant 0.18
fabG1 1673553 p.Asp38Glu missense_variant 0.14
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 2168551 p.Asn688Asp missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.54
fbiD 3339744 c.627A>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841590 c.-170G>A upstream_gene_variant 1.0
rpoA 3878591 c.-84C>G upstream_gene_variant 0.27
rpoA 3878641 c.-134C>G upstream_gene_variant 0.28
embC 4240409 p.Pro183Ala missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.1
embB 4246563 p.Leu17Trp missense_variant 0.1
embB 4246567 c.54G>T synonymous_variant 0.13
aftB 4268719 p.Asn40Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0