TB-Profiler result

Run: ERR4816050
Summary

Run ID: ERR4816050

Sample name:

Date: 01-04-2023 14:12:39

Number of reads: 690485

Percentage reads mapped: 99.57

Strain: lineage3.1.2.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.2 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 2155186 p.Gly309Asp missense_variant 0.14 isoniazid
katG 2155529 p.Glu195Lys missense_variant 0.17 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 5820 p.Leu194Pro missense_variant 0.1
gyrB 6683 p.Arg482Cys missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7534 p.Ala78Val missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7859 c.558A>C synonymous_variant 0.12
gyrA 7948 p.Leu216Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491527 p.Trp249Gly missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575672 p.Val109Met missense_variant 0.13
mshA 575676 p.Arg110His missense_variant 0.12
ccsA 620126 p.Gly79Ala missense_variant 0.25
ccsA 620317 p.Val143Ile missense_variant 0.14
ccsA 620351 p.Arg154His missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760436 c.630C>T synonymous_variant 0.18
rpoB 761766 p.Val654Met missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762517 p.Gly904Asp missense_variant 0.4
rpoB 762795 p.Asp997Tyr missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763141 p.Pro1112Leu missense_variant 0.13
rpoC 763386 p.Phe6Ser missense_variant 0.18
rpoC 764274 p.Phe302Ser missense_variant 0.14
rpoC 764435 p.Arg356Gly missense_variant 0.11
rpoC 764636 p.Asp423Asn missense_variant 0.13
rpoC 765526 c.2157C>A synonymous_variant 0.15
rpoC 766105 c.2736C>A synonymous_variant 0.12
rpoC 766673 p.Gly1102Cys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775898 c.2583G>A synonymous_variant 0.4
mmpL5 775987 p.His832Tyr missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778535 p.Asp124Gly missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781505 c.-55G>T upstream_gene_variant 0.11
rpsL 781590 p.Gly11Cys missense_variant 0.12
fbiC 1303134 c.204G>A synonymous_variant 0.22
fbiC 1303787 p.His286Leu missense_variant 0.2
fbiC 1304350 p.Glu474* stop_gained 0.12
Rv1258c 1407461 c.-121C>A upstream_gene_variant 0.18
atpE 1460962 c.-83G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471945 n.100G>T non_coding_transcript_exon_variant 0.12
rrs 1473362 n.1517C>T non_coding_transcript_exon_variant 0.17
rrl 1473709 n.52A>G non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>G non_coding_transcript_exon_variant 1.0
rrl 1475567 n.1914delA non_coding_transcript_exon_variant 0.25
rrl 1476171 n.2514G>T non_coding_transcript_exon_variant 0.12
rrl 1476730 n.3073G>T non_coding_transcript_exon_variant 0.12
inhA 1673442 c.-760G>T upstream_gene_variant 0.15
inhA 1674109 c.-93C>T upstream_gene_variant 0.22
rpsA 1833353 c.-189C>T upstream_gene_variant 0.25
rpsA 1833785 p.Val82Ile missense_variant 0.13
rpsA 1834126 c.585G>A synonymous_variant 0.11
rpsA 1834429 c.888C>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102663 p.Gly127Val missense_variant 0.14
ndh 2102696 p.Ile116Asn missense_variant 0.15
ndh 2103216 c.-174G>C upstream_gene_variant 0.12
katG 2153990 p.Val708Phe missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155953 c.159C>T synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170262 c.350delT frameshift_variant 0.29
PPE35 2170560 p.Gly18Val missense_variant 0.15
Rv1979c 2222076 c.1089C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518067 c.-48C>A upstream_gene_variant 0.12
kasA 2518295 p.Gly61Ser missense_variant 0.14
kasA 2518324 c.213_214delCA frameshift_variant 0.11
kasA 2518414 c.300C>T synonymous_variant 0.12
kasA 2518884 p.Arg257Leu missense_variant 0.15
eis 2715442 c.-110G>A upstream_gene_variant 0.33
eis 2715548 c.-216G>T upstream_gene_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726468 c.276G>T synonymous_variant 0.12
folC 2746228 c.1371C>T synonymous_variant 0.18
folC 2746517 p.Ala361Gly missense_variant 0.13
folC 2746748 p.Gly284Val missense_variant 0.33
folC 2746920 p.Ser227Pro missense_variant 0.17
pepQ 2859773 p.Asp216Tyr missense_variant 0.15
pepQ 2859782 p.Gln213* stop_gained 0.13
ribD 2986996 p.Ala53Asp missense_variant 0.2
ribD 2987546 c.708C>T synonymous_variant 0.2
Rv2752c 3064823 p.Val457Phe missense_variant 0.15
Rv2752c 3067053 c.-862C>T upstream_gene_variant 0.13
thyX 3067334 c.612C>G synonymous_variant 0.11
thyX 3067589 c.357G>A synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086928 p.Ala37Thr missense_variant 0.11
ald 3087476 c.657C>T synonymous_variant 1.0
fbiD 3339609 c.492G>A synonymous_variant 0.13
Rv3083 3448469 c.-35A>G upstream_gene_variant 0.12
Rv3083 3449601 p.Gln366His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474021 p.Tyr5* stop_gained 0.17
fprA 3474747 c.743delA frameshift_variant 0.13
Rv3236c 3612204 p.Lys305Glu missense_variant 0.15
fbiA 3640828 p.Gly96Cys missense_variant 0.13
fbiA 3640949 p.Trp136Leu missense_variant 0.13
fbiA 3641291 p.Lys250Thr missense_variant 0.14
fbiB 3642152 p.Lys206Asn missense_variant 0.11
fbiB 3642414 p.Pro294Thr missense_variant 0.25
alr 3840859 p.Val188Ile missense_variant 0.15
alr 3841587 c.-167G>A upstream_gene_variant 0.12
rpoA 3877882 p.Ala209Val missense_variant 0.14
clpC1 4038270 p.Pro812His missense_variant 0.33
clpC1 4038425 c.2280C>T synonymous_variant 0.22
embC 4239848 c.-15G>T upstream_gene_variant 0.18
embC 4239901 c.39G>A synonymous_variant 0.12
embC 4240613 p.Leu251Met missense_variant 0.25
embC 4241195 p.Ser445Pro missense_variant 0.17
embC 4241644 c.1782G>A synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242239 p.Asp793Asn missense_variant 0.15
embC 4242578 p.Ala906Ser missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243328 c.96G>C synonymous_variant 0.22
embA 4245189 p.Leu653Met missense_variant 0.22
embA 4245254 c.2022C>T synonymous_variant 0.18
embA 4246108 p.Pro959His missense_variant 0.11
embB 4246644 p.Thr44Arg missense_variant 0.4
embB 4248506 p.Gly665Trp missense_variant 0.15
embB 4249036 c.2523G>T synonymous_variant 0.12
embB 4249550 p.Arg1013Cys missense_variant 0.18
aftB 4267019 c.1818G>C synonymous_variant 0.14
aftB 4268652 p.Ala62Gly missense_variant 0.12
aftB 4268845 c.-9T>C upstream_gene_variant 0.2
ubiA 4269070 p.Phe255Tyr missense_variant 0.15
ubiA 4269095 p.Trp247Arg missense_variant 0.14
ethA 4326130 p.Lys448Asn missense_variant 0.11
ethA 4326176 p.Glu433Ala missense_variant 1.0
ethA 4328049 c.-576C>T upstream_gene_variant 0.17
ethA 4328200 c.-727C>A upstream_gene_variant 0.13
ethA 4328213 c.-740C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407531 c.672G>C synonymous_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408017 c.186T>G synonymous_variant 0.14
gid 4408034 p.Glu57* stop_gained 0.2
gid 4408263 c.-61G>T upstream_gene_variant 0.17