TB-Profiler result

Run: ERR4820447
Summary

Run ID: ERR4820447

Sample name:

Date: 01-04-2023 16:41:17

Number of reads: 501102

Percentage reads mapped: 99.55

Strain: lineage3.1.2

Drug-resistance: Sensitive

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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
lineage3.1.2 East-African-Indian CAS;CAS2 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
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 8847 p.Val516Phe missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9778 p.Asn826Ile missense_variant 0.17
fgd1 490648 c.-135C>A upstream_gene_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620506 p.Pro206Ser missense_variant 0.11
ccsA 620842 p.His318Asn missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762925 p.Thr1040Asn missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765966 p.Arg866His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775720 p.Val921Leu missense_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777133 p.Val450Ile missense_variant 0.1
mmpL5 777155 c.1326G>C synonymous_variant 0.12
mmpL5 777944 c.537A>T synonymous_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801390 c.582C>A synonymous_variant 0.15
fbiC 1303158 c.231delG frameshift_variant 0.13
fbiC 1304099 p.Gln390Pro missense_variant 0.13
Rv1258c 1407540 c.-200C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472638 n.793A>G non_coding_transcript_exon_variant 0.2
rpsA 1834166 p.Gly209Cys missense_variant 0.12
rpsA 1834222 p.Asp227Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918696 p.Ala253Pro missense_variant 1.0
katG 2153965 p.Ala716Val missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.1
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169347 c.1265delT frameshift_variant 0.15
Rv1979c 2222684 p.Trp161Arg missense_variant 0.12
Rv1979c 2223031 p.Pro45His missense_variant 0.12
Rv1979c 2223257 c.-93G>C upstream_gene_variant 1.0
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 2518949 p.Ala279Ser missense_variant 0.13
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747130 p.Ala157Thr missense_variant 0.13
Rv2752c 3064531 p.Thr554Met missense_variant 0.25
thyA 3074009 p.Ala155Thr missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475052 p.Asn349Thr missense_variant 1.0
fprA 3475297 p.Arg431Trp missense_variant 0.15
whiB7 3568737 c.-58C>T upstream_gene_variant 0.14
fbiA 3640525 c.-17delA upstream_gene_variant 0.17
fbiA 3640936 c.395delT frameshift_variant 0.11
fbiB 3642469 c.938_940dupTGA disruptive_inframe_insertion 0.18
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3877804 p.Gly235Glu missense_variant 0.11
rpoA 3878143 p.Gly122Asp missense_variant 0.13
rpoA 3878218 p.Leu97Pro missense_variant 0.1
ddn 3986678 c.-165delA upstream_gene_variant 0.18
embC 4241468 p.Ala536Thr missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247356 c.843C>T synonymous_variant 0.14
embB 4248241 c.1728C>G synonymous_variant 1.0
aftB 4267619 c.1217delG frameshift_variant 0.33
ubiA 4269151 p.Ala228Val missense_variant 0.25
ethA 4326548 p.Lys309Arg missense_variant 0.11
ethA 4327461 p.Leu5Ile missense_variant 0.14
ethR 4327693 p.Asp49Asn missense_variant 1.0
ethR 4327970 p.Phe141Ser missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408147 p.Ala19Val missense_variant 1.0
gid 4408342 c.-140C>T upstream_gene_variant 0.11