TB-Profiler result

Run: ERR4814416
Summary

Run ID: ERR4814416

Sample name:

Date: 01-04-2023 13:16:59

Number of reads: 2295479

Percentage reads mapped: 99.35

Strain: lineage1.1.2

Drug-resistance: HR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6995 p.Glu586Lys missense_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
mshA 576108 p.Ala254Gly missense_variant 0.17
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 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777323 c.1158C>T synonymous_variant 1.0
mmpL5 777951 p.Ala177Val missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801288 c.480G>A synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471850 n.5G>T non_coding_transcript_exon_variant 1.0
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.17
rrs 1473079 n.1234G>T non_coding_transcript_exon_variant 0.18
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.23
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.21
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.19
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.19
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.16
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.16
rrl 1473771 n.114T>C non_coding_transcript_exon_variant 0.11
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.22
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.25
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.25
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.25
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.2
rrl 1474272 n.615C>T non_coding_transcript_exon_variant 0.2
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.2
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.25
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.25
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918545 p.Gln202His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169063 p.Met517Lys missense_variant 0.18
PPE35 2170516 p.Gly33Arg 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 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_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
Rv3236c 3612496 c.621C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_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 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338278 p.Pro82Ser 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 4407873 c.330G>T synonymous_variant 1.0