TB-Profiler result

Run: ERR2516869
Summary

Run ID: ERR2516869

Sample name:

Date: 31-03-2023 21:47:32

Number of reads: 1218069

Percentage reads mapped: 99.7

Strain: lineage3

Drug-resistance: HR-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
katG 2155031 c.1080_1081insA frameshift_variant 0.91 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 6579 p.Ser447Tyr missense_variant 0.17
gyrB 7156 p.Asp639Glu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7407 p.Ile36Phe missense_variant 0.15
gyrA 7428 p.Glu43* stop_gained 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8816 c.1515C>A synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491295 c.513C>A synonymous_variant 0.25
fgd1 491479 p.Ile233Val missense_variant 0.18
fgd1 491651 p.Pro290His missense_variant 0.18
fgd1 491655 p.Asp291Glu missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759742 c.-65G>T upstream_gene_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759750 c.-57G>T upstream_gene_variant 0.22
rpoB 761965 p.Trp720Leu missense_variant 0.17
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 777779 c.702G>T synonymous_variant 0.17
mmpR5 779375 p.Pro129Gln missense_variant 0.18
mmpS5 779555 c.-650C>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781517 c.-43C>G upstream_gene_variant 0.14
embR 1417038 p.Ser104Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472145 n.300G>T non_coding_transcript_exon_variant 0.14
rrl 1474385 n.728C>A non_coding_transcript_exon_variant 0.17
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.17
rrl 1476111 n.2454G>T non_coding_transcript_exon_variant 0.18
rrl 1476118 n.2461G>T non_coding_transcript_exon_variant 0.18
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.18
fabG1 1673792 p.Arg118Leu missense_variant 0.2
inhA 1674630 c.429C>A synonymous_variant 0.15
inhA 1674701 p.Ala167Glu missense_variant 0.15
rpsA 1834665 p.Pro375Gln missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102178 p.Leu289Ile missense_variant 0.22
ndh 2102269 c.774C>A synonymous_variant 0.2
ndh 2102604 c.439T>C synonymous_variant 0.13
ndh 2102610 c.433T>C synonymous_variant 0.13
katG 2154103 p.Pro670His missense_variant 0.15
katG 2154528 p.Phe528Leu missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154767 p.Leu449Ile missense_variant 0.14
katG 2154807 c.1305C>A synonymous_variant 0.33
katG 2155212 p.Trp300Cys missense_variant 0.15
katG 2155920 c.192T>C synonymous_variant 0.11
PPE35 2167711 p.Ser968Pro missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168270 c.2343G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289259 c.-18C>A upstream_gene_variant 0.17
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290105 c.-864G>T upstream_gene_variant 0.29
kasA 2518590 p.Gly159Val missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726118 c.-75T>C upstream_gene_variant 0.12
folC 2746562 p.Pro346His missense_variant 0.17
pepQ 2859829 p.Gly197Val missense_variant 0.15
Rv2752c 3064806 c.1386G>T synonymous_variant 0.15
Rv2752c 3064860 c.1332G>T synonymous_variant 0.15
Rv2752c 3064917 c.1275C>T synonymous_variant 1.0
Rv2752c 3065898 c.294C>A synonymous_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448626 c.123G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474189 c.183G>A synonymous_variant 0.12
fprA 3474273 c.267G>A synonymous_variant 0.13
fprA 3474843 p.Lys279Asn missense_variant 0.14
clpC1 4039522 p.Leu395Met missense_variant 0.22
clpC1 4039553 c.1152C>A synonymous_variant 0.2
clpC1 4039794 p.Ala304Asp missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245699 p.Gly823Trp missense_variant 0.19
embB 4248962 p.Ala817Ser missense_variant 0.15
embB 4249630 c.3117C>A synonymous_variant 0.18
embB 4249721 p.Leu1070Met missense_variant 0.14
aftB 4268257 p.Gly194Trp missense_variant 0.2
aftB 4268558 c.279G>C synonymous_variant 0.1
aftB 4268780 p.Trp19Cys missense_variant 0.23
ubiA 4269073 p.Pro254Gln missense_variant 0.2
ubiA 4270032 c.-199C>A upstream_gene_variant 0.15
ethA 4327041 p.Glu145* stop_gained 0.2
ethA 4327058 p.Gly139Val missense_variant 0.18
ethR 4327162 c.-387C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407688 p.Arg172Leu missense_variant 0.15
gid 4407913 p.Arg97Leu missense_variant 0.33
gid 4408459 c.-257G>T upstream_gene_variant 0.21