TB-Profiler result

Run: ERR3077990
Summary

Run ID: ERR3077990

Sample name:

Date: 01-04-2023 00:15:10

Number of reads: 7264706

Percentage reads mapped: 99.21

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA RD239 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
rpoB 761139 p.His445Tyr missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247469 p.Tyr319Cys missense_variant 0.99 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761728 p.Ser641Asn missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.99
rpoC 763886 c.517C>A synonymous_variant 0.99
rpoC 764075 p.Val236Ile missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777817 p.Val222Phe missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475102 n.1445C>T non_coding_transcript_exon_variant 1.0
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 2168205 p.Pro803Gln missense_variant 0.99
PPE35 2169029 p.Asp528Asn missense_variant 0.15
PPE35 2169041 c.1572G>A synonymous_variant 0.43
PPE35 2169044 c.1569G>C synonymous_variant 0.51
PPE35 2169047 p.Ile522Val missense_variant 0.49
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.49
PPE35 2169059 c.1554G>A synonymous_variant 0.51
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.51
PPE35 2169068 c.1545G>T synonymous_variant 0.52
PPE35 2169071 c.1542A>G synonymous_variant 0.42
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.99
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475319 p.Gly438Glu missense_variant 1.0
Rv3236c 3613041 c.76C>A synonymous_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239899 c.37C>A synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243246 p.Gly5Asp missense_variant 1.0
embA 4243532 c.300C>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246275 p.Ala1015Thr missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.99
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269469 p.Pro122Gln missense_variant 0.99
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 0.99
ethA 4326624 p.Pro284Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408124 p.Ala27Pro missense_variant 1.0