TB-Profiler result

Run: ERR495176
Summary

Run ID: ERR495176

Sample name:

Date: 01-04-2023 21:41:10

Number of reads: 768250

Percentage reads mapped: 99.29

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
ahpC 2726206 p.Thr5Ile missense_variant 0.25 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 5046 c.-194T>C upstream_gene_variant 0.15
gyrB 5088 c.-151_-148delAGGA upstream_gene_variant 0.17
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5842 p.Asn201Lys missense_variant 0.18
gyrB 5847 p.Gly203Val missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7499 c.198G>A synonymous_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8098 p.Arg266His missense_variant 0.13
gyrA 8111 c.810G>A synonymous_variant 0.13
gyrA 9074 c.1773G>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491171 p.Ala130Gly missense_variant 1.0
fgd1 491300 p.Tyr173Phe missense_variant 0.33
mshA 575258 c.-90G>T upstream_gene_variant 0.17
ccsA 620202 c.312G>A synonymous_variant 0.25
ccsA 620605 p.Val239Ile missense_variant 0.15
rpoB 759781 c.-26C>T upstream_gene_variant 0.13
rpoB 760364 c.558C>T synonymous_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765528 p.Gly720Asp missense_variant 0.21
rpoC 765638 p.Glu757Lys missense_variant 0.17
rpoC 766052 p.Arg895Cys missense_variant 0.22
rpoC 767040 p.Ala1224Val missense_variant 0.14
rpoC 767146 c.3777G>C synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775732 p.Asp917Tyr missense_variant 0.2
mmpL5 776894 c.1587T>A synonymous_variant 0.25
mmpL5 777348 p.Gly378Asp missense_variant 0.29
mmpL5 778849 c.-369C>T upstream_gene_variant 0.29
mmpR5 779309 p.Arg107His missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800959 p.Gln51* stop_gained 0.25
rplC 801378 c.570C>T synonymous_variant 0.18
fbiC 1302981 c.51A>T synonymous_variant 0.17
fbiC 1302989 p.Gln20Leu missense_variant 0.17
Rv1258c 1406195 p.Ala382Val missense_variant 0.25
Rv1258c 1406992 p.Gly117Ser missense_variant 0.25
embR 1416388 c.960A>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474134 n.477G>A non_coding_transcript_exon_variant 0.18
rrl 1474859 n.1202A>G non_coding_transcript_exon_variant 0.33
rrl 1475893 n.2236A>G non_coding_transcript_exon_variant 0.18
rpsA 1833373 c.-169G>A upstream_gene_variant 0.2
rpsA 1834437 p.Gly299Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918507 p.Gly190Ser missense_variant 0.25
ndh 2101795 c.1248G>A synonymous_variant 0.2
ndh 2102614 c.429C>T synonymous_variant 0.25
ndh 2102905 c.138C>T synonymous_variant 0.17
katG 2156273 c.-162T>G upstream_gene_variant 0.22
PPE35 2170478 c.135C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518853 p.Leu247Phe missense_variant 0.29
kasA 2518883 p.Arg257Cys missense_variant 0.33
folC 2747146 c.453G>A synonymous_variant 0.14
folC 2747483 p.Pro39Leu missense_variant 0.33
pepQ 2860077 c.342G>A synonymous_variant 0.29
Rv2752c 3065153 p.Ala347Thr missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074091 c.381C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087679 p.Thr287Met missense_variant 0.22
Rv3083 3449845 p.Gln448* stop_gained 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474325 p.Gln107Lys missense_variant 0.25
fprA 3475062 c.1056C>A synonymous_variant 0.15
whiB7 3568592 p.Ala30Thr missense_variant 0.2
whiB7 3568827 c.-148G>A upstream_gene_variant 0.29
whiB7 3568845 c.-166G>A upstream_gene_variant 0.33
fbiB 3642488 c.954G>A synonymous_variant 0.13
alr 3840790 p.Gln211* stop_gained 0.18
alr 3841361 c.60G>A synonymous_variant 0.17
rpoA 3878058 c.450G>A synonymous_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038493 p.Val738Ile missense_variant 0.22
panD 4044241 p.Thr14Lys missense_variant 0.33
embC 4241668 c.1806G>A synonymous_variant 0.15
embC 4242188 p.Ala776Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244172 c.940C>T synonymous_variant 0.67
embA 4244371 p.Arg380His missense_variant 0.17
embA 4245709 p.Ala826Val missense_variant 0.18
embB 4246247 c.-267C>T upstream_gene_variant 0.25
embB 4247413 c.900C>T synonymous_variant 0.2
aftB 4268220 p.Thr206Ile missense_variant 0.17
ethR 4326673 c.-876C>T upstream_gene_variant 0.25
ethA 4328318 c.-845G>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0