TB-Profiler result

Run: ERR4798523
Summary

Run ID: ERR4798523

Sample name:

Date: 01-04-2023 08:25:59

Number of reads: 1971070

Percentage reads mapped: 50.52

Strain: lineage1.2.2.2

Drug-resistance: MDR-TB

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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
embB 4247730 p.Gly406Ala 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 5075 c.-165C>T upstream_gene_variant 0.99
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765816 p.Thr816Met missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777431 c.1047_1049delCGC disruptive_inframe_deletion 1.0
mmpS5 779625 c.-720G>A upstream_gene_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
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.11
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.29
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.52
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.56
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.54
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.54
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.54
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.52
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.48
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.48
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.48
rrs 1472582 n.738_739delTA non_coding_transcript_exon_variant 0.5
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.52
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.53
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.59
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.41
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.36
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.38
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.35
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.35
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.55
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.54
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.58
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.53
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.29
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.21
rrs 1472842 n.997G>A non_coding_transcript_exon_variant 0.2
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.2
rrl 1475792 n.2135G>T non_coding_transcript_exon_variant 0.18
rrl 1475935 n.2278T>A non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
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 0.98
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747468 p.Asp44Gly missense_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
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267960 p.Val293Met missense_variant 0.97
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407799 p.Val135Ala missense_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0