TB-Profiler result

Run: ERR4817033
Summary

Run ID: ERR4817033

Sample name:

Date: 01-04-2023 14:45:58

Number of reads: 730359

Percentage reads mapped: 99.34

Strain: lineage1.1.3.3

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
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.3 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val 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 5121 c.-119A>G upstream_gene_variant 0.13
gyrB 5769 p.Pro177Gln missense_variant 0.17
gyrB 5792 p.Tyr185His missense_variant 0.15
gyrB 6112 p.Met291Ile 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 9077 c.1776C>T synonymous_variant 0.14
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 575435 p.Pro30Thr missense_variant 0.12
mshA 576455 p.Val370Met missense_variant 0.25
ccsA 620539 p.Arg217Trp missense_variant 0.25
rpoB 760577 p.Glu257Asp missense_variant 0.12
rpoB 760787 c.981G>A synonymous_variant 0.2
rpoB 762309 p.His835Asn missense_variant 0.2
rpoB 762499 p.Met898Thr missense_variant 0.15
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 764293 c.924G>T synonymous_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766898 p.Pro1177Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 c.2475C>T synonymous_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776423 p.Asp686Glu missense_variant 0.2
mmpL5 776826 p.Glu552Gly missense_variant 1.0
mmpR5 778292 c.-698C>T upstream_gene_variant 0.12
mmpL5 778407 p.Pro25His missense_variant 0.14
mmpS5 778565 p.Cys114Phe missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781428 c.-132C>T upstream_gene_variant 0.18
rpsL 781471 c.-89A>G upstream_gene_variant 0.17
rpsL 781521 c.-39A>T upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473628 n.-30T>C upstream_gene_variant 0.2
rrl 1474443 n.786T>C non_coding_transcript_exon_variant 0.29
inhA 1673625 c.-577C>T upstream_gene_variant 0.15
tlyA 1917812 c.-128G>A upstream_gene_variant 0.12
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168124 p.Gly830Glu missense_variant 1.0
PPE35 2169630 p.Asn328Ser missense_variant 1.0
PPE35 2169743 c.870G>A synonymous_variant 0.14
PPE35 2169757 p.Asn286Asp missense_variant 1.0
PPE35 2170524 p.Ala30Asp missense_variant 0.14
Rv1979c 2222058 c.1107C>T synonymous_variant 0.18
Rv1979c 2222283 c.882C>T synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289435 c.-194G>T upstream_gene_variant 0.29
pncA 2289621 c.-380C>T upstream_gene_variant 0.18
pncA 2289868 c.-627G>T upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519100 p.Ala329Val missense_variant 1.0
eis 2714377 p.Thr319Met missense_variant 0.13
ahpC 2726001 c.-192T>A upstream_gene_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726100 c.-92_-91delGT upstream_gene_variant 0.11
ribD 2987263 p.Val142Ala missense_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064671 c.1521C>A synonymous_variant 0.12
ald 3086693 c.-126delC upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087716 c.897G>A synonymous_variant 0.25
Rv3083 3448683 p.Phe60Leu missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449709 c.1206C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474524 p.Leu173Ser missense_variant 0.12
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568860 c.-181A>C upstream_gene_variant 0.13
fbiB 3640971 c.-564G>A upstream_gene_variant 0.14
fbiA 3641370 p.Tyr276* stop_gained 0.14
fbiB 3641707 p.Gly58Ala missense_variant 0.11
alr 3840493 c.928C>T synonymous_variant 1.0
alr 3841349 c.72C>A synonymous_variant 1.0
clpC1 4040168 c.537G>A synonymous_variant 0.13
clpC1 4040496 p.Gly70Val missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043904 c.378A>G synonymous_variant 0.11
embC 4240207 c.345G>A synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241811 p.Trp650* stop_gained 0.12
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
embA 4246200 p.Gln990Lys missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248429 p.Cys639Tyr missense_variant 0.14
aftB 4267431 p.Ser469Leu missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326516 p.Phe320Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338648 c.-127A>G upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407677 p.Arg176Cys missense_variant 0.18
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0