TB-Profiler result

Run: ERR4407538
Summary

Run ID: ERR4407538

Sample name:

Date: 01-04-2023 05:49:07

Number of reads: 695271

Percentage reads mapped: 98.87

Strain: lineage4.3.4.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
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 6128 p.Tyr297His missense_variant 0.12
gyrB 6807 p.Arg523His missense_variant 0.12
gyrB 6821 p.Val528Met missense_variant 0.18
gyrA 6926 c.-376T>C upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7512 p.Ala71Thr missense_variant 0.12
gyrA 7536 p.Glu79Lys missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491490 c.708C>T synonymous_variant 0.17
mshA 575248 c.-100C>T upstream_gene_variant 0.14
mshA 575402 p.Val19Ile missense_variant 0.12
mshA 575592 p.Arg82Leu missense_variant 0.12
ccsA 620259 c.369C>T synonymous_variant 0.2
ccsA 620616 c.726C>T synonymous_variant 0.11
rpoB 759620 c.-187A>C upstream_gene_variant 0.43
rpoB 760959 p.Val385Phe missense_variant 0.12
rpoC 764541 p.Val391Gly missense_variant 0.2
rpoC 764543 p.Thr392Asp missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765097 p.Met576Ile missense_variant 0.12
rpoC 765764 p.Ile799Phe missense_variant 0.12
rpoC 766999 c.3630C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775929 p.Asn851Ser missense_variant 0.11
mmpR5 778421 c.-569C>T upstream_gene_variant 0.12
mmpL5 778935 c.-455G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800628 c.-181G>A upstream_gene_variant 0.17
rplC 800674 c.-135A>G upstream_gene_variant 0.12
fbiC 1303226 p.Arg99Gln missense_variant 0.14
fbiC 1303897 p.Leu323Met missense_variant 0.15
fbiC 1304801 p.Arg624Leu missense_variant 0.15
Rv1258c 1406493 p.Ile283Thr missense_variant 0.1
embR 1416189 p.Gly387Cys missense_variant 0.17
embR 1417150 c.198G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471673 n.-173C>A upstream_gene_variant 0.2
rrl 1473495 n.-163T>C upstream_gene_variant 0.33
rrl 1473658 n.1T>C non_coding_transcript_exon_variant 0.25
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.5
inhA 1673973 c.-229G>T upstream_gene_variant 0.2
inhA 1674897 p.Met232Ile missense_variant 0.12
rpsA 1834364 p.Ser275Pro missense_variant 0.11
rpsA 1834629 p.Lys363Arg missense_variant 0.1
tlyA 1917797 c.-143C>A upstream_gene_variant 0.14
tlyA 1917827 c.-113C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103035 p.Pro3His missense_variant 0.17
katG 2156358 c.-247G>A upstream_gene_variant 0.12
PPE35 2167724 c.2889G>A synonymous_variant 0.11
PPE35 2167814 c.2799C>T synonymous_variant 0.11
PPE35 2168336 p.Leu759Phe missense_variant 0.12
PPE35 2169251 c.1362C>T synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170803 c.-191G>A upstream_gene_variant 1.0
Rv1979c 2221877 p.Val430Leu missense_variant 0.13
Rv1979c 2223123 c.42G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289569 c.-328G>T upstream_gene_variant 0.2
pncA 2289723 c.-482C>A upstream_gene_variant 0.13
eis 2714877 p.Asp152Glu missense_variant 0.12
eis 2715037 p.Ala99Glu missense_variant 0.13
eis 2715488 c.-156C>A upstream_gene_variant 0.2
eis 2715500 c.-168T>A upstream_gene_variant 0.14
ahpC 2726424 p.Arg78Gly missense_variant 0.18
ahpC 2726596 p.Thr135Asn missense_variant 0.14
folC 2746281 p.Ile440Val missense_variant 0.22
folC 2746827 c.772C>A synonymous_variant 0.12
folC 2747025 p.Ala192Ser missense_variant 0.15
folC 2747614 c.-16G>T upstream_gene_variant 0.25
folC 2747643 c.-45G>A upstream_gene_variant 0.33
ribD 2987132 p.Met98Ile missense_variant 0.13
ribD 2987503 p.Gly222Val missense_variant 0.11
Rv2752c 3064797 c.1395G>T synonymous_variant 0.18
Rv2752c 3067027 c.-836C>T upstream_gene_variant 0.11
Rv2752c 3067041 c.-850C>G upstream_gene_variant 1.0
Rv2752c 3067113 c.-922C>G upstream_gene_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087763 p.Asn315Ser missense_variant 0.33
ald 3087803 c.984C>T synonymous_variant 0.25
fbiD 3339143 c.28_35delATCGGCTT frameshift_variant 0.13
fbiD 3339156 c.40_41insAGCCGATA frameshift_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474619 p.Ala205Thr missense_variant 0.13
fprA 3475017 p.Gln337His missense_variant 0.11
fprA 3475033 p.Asn343Asp missense_variant 0.12
whiB7 3568785 c.-106A>C upstream_gene_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612812 p.Thr102Lys missense_variant 0.15
fbiB 3640617 c.-918G>T upstream_gene_variant 0.13
fbiA 3640892 p.Gln117Arg missense_variant 0.12
fbiA 3640912 p.Pro124Thr missense_variant 0.2
fbiA 3641075 p.Ala178Asp missense_variant 0.13
fbiA 3641107 p.Gly189Ser missense_variant 0.13
fbiA 3641350 p.Ala270Ser missense_variant 0.14
fbiB 3642695 c.1161G>A synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038316 p.Gly797Cys missense_variant 0.13
clpC1 4038464 p.Met747Ile missense_variant 0.12
clpC1 4038934 p.Ala591Thr missense_variant 0.14
clpC1 4040122 p.Lys195Glu missense_variant 0.12
embC 4240394 p.Glu178* stop_gained 0.15
embC 4241722 c.1860C>G synonymous_variant 0.12
embC 4241761 c.1899G>A synonymous_variant 0.13
embC 4242584 p.Ala908Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243424 c.196delG frameshift_variant 0.11
embA 4243704 p.Gly158Ser missense_variant 0.12
embA 4243926 c.696_697delCC frameshift_variant 0.22
embA 4244659 p.Leu476Pro missense_variant 0.11
embA 4244744 p.Phe504Leu missense_variant 0.12
embB 4245755 c.-759C>T upstream_gene_variant 0.12
embA 4245803 p.Tyr857* stop_gained 0.12
embB 4245860 c.-654C>A upstream_gene_variant 0.12
embB 4246556 p.Ala15Ser missense_variant 0.12
aftB 4266961 c.1876C>A synonymous_variant 0.12
aftB 4267167 p.Gln557Arg missense_variant 0.25
aftB 4268133 p.Leu235Arg missense_variant 0.18
ubiA 4269198 p.Ser212Arg missense_variant 0.15
ethA 4327430 p.Ser15Phe missense_variant 1.0
ethR 4327589 c.43dupC frameshift_variant 0.15
ethA 4328412 c.-939G>T upstream_gene_variant 0.12
whiB6 4338383 p.Asp47Tyr missense_variant 0.12
whiB6 4338388 p.Pro45His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407780 c.423G>T synonymous_variant 0.12
gid 4407857 p.Arg116Gly missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 1.0