TB-Profiler result

Run: ERR2245332
Summary

Run ID: ERR2245332

Sample name:

Date: 31-03-2023 17:38:35

Number of reads: 3586893

Percentage reads mapped: 98.55

Strain: lineage3.1.1

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 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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 2155795 p.Ala106Val missense_variant 0.15 isoniazid
embC 4240592 p.Ala244Thr missense_variant 0.22 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575356 c.9T>A synonymous_variant 0.12
mshA 575548 c.201C>A synonymous_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.28
mshA 576111 p.Ala255Gly missense_variant 0.25
ccsA 619729 c.-162G>T upstream_gene_variant 0.22
ccsA 620420 p.Ser177* stop_gained 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 0.97
rpoB 760564 p.Arg253Leu missense_variant 0.14
rpoB 760613 p.Leu269Phe missense_variant 0.12
rpoB 761611 p.Gly602Val missense_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764318 p.Val317Ile missense_variant 0.17
rpoC 765407 p.Gly680Cys missense_variant 0.13
rpoC 766325 p.Gly986Ser missense_variant 0.18
rpoC 766355 p.Gly996Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777297 p.Val395Gly missense_variant 0.29
mmpL5 778170 p.Ala104Asp missense_variant 0.15
mmpR5 779198 p.Asn70Ser missense_variant 0.12
mmpR5 779293 p.Ala102Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305010 p.Val694Met missense_variant 0.13
fbiC 1305019 p.Ala697Thr missense_variant 0.14
Rv1258c 1406299 p.Val348Ile missense_variant 0.2
Rv1258c 1406468 p.Met291Ile missense_variant 0.2
atpE 1461040 c.-4delG upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473004 n.1159T>G non_coding_transcript_exon_variant 0.67
rrl 1474849 n.1192G>T non_coding_transcript_exon_variant 1.0
rpsA 1834936 c.1395C>A synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918130 p.Ser64* stop_gained 0.4
ndh 2102071 c.972C>G synonymous_variant 0.11
ndh 2103157 c.-115G>T upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518663 c.549T>G synonymous_variant 0.22
eis 2714331 c.1002T>C synonymous_variant 0.2
eis 2715560 c.-228T>C upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746488 p.Asp371Tyr missense_variant 0.17
pepQ 2859509 p.Glu304* stop_gained 0.12
pepQ 2859691 p.Ala243Asp missense_variant 0.12
pepQ 2860592 c.-174T>A upstream_gene_variant 0.33
Rv2752c 3064665 c.1527C>G synonymous_variant 0.12
thyX 3067326 p.Glu207Gly missense_variant 0.18
thyX 3067673 c.273C>T synonymous_variant 0.17
thyX 3067960 c.-15G>T upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087209 c.390T>C synonymous_variant 0.13
fbiD 3338950 c.-168C>T upstream_gene_variant 0.12
fbiD 3338963 c.-155C>T upstream_gene_variant 0.12
fbiD 3339454 c.337C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612768 p.Ala117Ser missense_variant 0.14
fbiB 3642681 p.Ala383Thr missense_variant 0.12
alr 3840370 p.Gly351Cys missense_variant 0.15
rpoA 3877657 p.Leu284Pro missense_variant 0.1
rpoA 3878490 c.18C>G synonymous_variant 0.25
clpC1 4038316 p.Gly797Ser missense_variant 0.22
clpC1 4039328 c.1377A>T synonymous_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.14
embC 4240027 c.165C>A synonymous_variant 0.23
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240186 c.324G>A synonymous_variant 0.15
embC 4241250 p.Arg463Leu missense_variant 0.18
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242223 c.2361C>G synonymous_variant 0.13
embC 4242258 p.Val799Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243398 p.Thr56Pro missense_variant 0.25
embA 4244192 c.960C>A synonymous_variant 1.0
embA 4246273 p.Thr1014Lys missense_variant 0.14
embB 4246846 p.Leu111Phe missense_variant 0.13
embB 4246888 c.375C>A synonymous_variant 0.13
embB 4249691 p.Asp1060Asn missense_variant 0.14
aftB 4267286 p.His517Gln missense_variant 0.13
aftB 4267931 c.906C>A synonymous_variant 0.4
aftB 4268211 p.Arg209His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407533 p.Ala224Ser missense_variant 0.15
gid 4407560 p.Ser215Ala missense_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407625 p.Ala193Glu missense_variant 0.14