TB-Profiler result

Run: ERR7801221

Summary

Run ID: ERR7801221

Sample name:

Date: 02-04-2023 05:59:27

Number of reads: 903990

Percentage reads mapped: 99.43

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 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
katG 2155339 p.Asn258Ser missense_variant 0.13 isoniazid
embB 4247473 p.Phe320Leu missense_variant 0.14 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
gyrB 5464 c.225C>A synonymous_variant 0.18
gyrB 5769 p.Pro177His missense_variant 0.15
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 6458 c.1220delT frameshift_variant 0.12
gyrA 7274 c.-28C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7861 p.Thr187Asn missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620063 p.Ser58Ile missense_variant 0.15
rpoB 759680 c.-127G>A upstream_gene_variant 0.2
rpoB 761202 p.Val466Phe missense_variant 0.11
rpoB 761280 p.Gly492Cys missense_variant 0.14
rpoB 761333 c.1527G>A synonymous_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765883 c.2514C>A synonymous_variant 0.15
rpoC 766522 c.3153C>T synonymous_variant 0.29
rpoC 766982 p.Pro1205Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776939 c.1542C>T synonymous_variant 0.12
mmpL5 777172 p.His437Tyr missense_variant 0.17
mmpL5 777570 p.Gly304Val missense_variant 0.33
mmpL5 777611 c.870G>T synonymous_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303209 c.279G>T synonymous_variant 0.14
fbiC 1304571 c.1641G>T synonymous_variant 0.22
fbiC 1304599 p.Ile557Val missense_variant 0.11
fbiC 1305019 p.Ala697Ser missense_variant 0.12
Rv1258c 1406419 c.922C>T synonymous_variant 0.29
Rv1258c 1407449 c.-109G>C upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472403 n.558G>T non_coding_transcript_exon_variant 0.14
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.13
rrl 1473950 n.293G>A non_coding_transcript_exon_variant 0.25
rrl 1474198 n.541G>T non_coding_transcript_exon_variant 0.15
rrl 1475013 n.1356G>T non_coding_transcript_exon_variant 0.29
rrl 1475635 n.1978G>T non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
inhA 1674696 p.Lys165Asn missense_variant 0.15
inhA 1674880 p.Pro227Thr missense_variant 0.18
rpsA 1833524 c.-18C>A upstream_gene_variant 0.13
tlyA 1917841 c.-99C>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155390 p.Pro241His missense_variant 0.18
katG 2156404 c.-293G>T upstream_gene_variant 0.15
PPE35 2168266 p.Gly783Trp missense_variant 0.14
PPE35 2168818 p.Gly599Ser missense_variant 0.14
PPE35 2170105 p.Leu170Ile missense_variant 0.15
Rv1979c 2221738 p.Asp476Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518202 p.Glu30* stop_gained 0.2
kasA 2518649 p.Ala179Ser missense_variant 0.12
kasA 2519052 p.Thr313Lys missense_variant 0.13
kasA 2519089 c.975C>A synonymous_variant 0.15
kasA 2519264 c.1151delT frameshift_variant 0.15
kasA 2519305 c.1191A>T synonymous_variant 0.14
folC 2746673 p.Val309Ala missense_variant 0.11
folC 2747446 p.Ser51Arg missense_variant 0.17
pepQ 2859601 c.817delG frameshift_variant 0.13
thyX 3067693 p.Ile85Val missense_variant 0.12
thyX 3067750 p.Asp66Tyr missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086650 c.-170C>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086846 c.32delA frameshift_variant 0.18
fbiD 3339371 p.Pro85His missense_variant 0.18
fbiD 3339604 p.Gly163Trp missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474388 p.Phe128Ile missense_variant 0.18
whiB7 3568558 p.Thr41Lys missense_variant 0.14
whiB7 3568597 p.Trp28Leu missense_variant 0.14
whiB7 3568797 c.-118G>T upstream_gene_variant 0.17
Rv3236c 3612009 p.Ala370Thr missense_variant 0.9
Rv3236c 3612228 p.Leu297Met missense_variant 0.12
Rv3236c 3612790 p.Trp109Cys missense_variant 0.12
Rv3236c 3613120 c.-4A>T upstream_gene_variant 0.12
Rv3236c 3613193 c.-77C>T upstream_gene_variant 0.17
fbiB 3641770 c.238dupG frameshift_variant 0.17
fbiB 3641908 p.Pro125His missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841470 c.-50G>T upstream_gene_variant 0.12
alr 3841503 c.-83G>A upstream_gene_variant 0.13
rpoA 3878268 c.240C>A synonymous_variant 0.14
rpoA 3878319 p.Phe63Leu missense_variant 0.17
ddn 3987235 p.Pro131Gln missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039882 p.Glu275Gln missense_variant 0.14
embC 4242599 p.Gly913Trp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244847 p.Gly539Cys missense_variant 0.33
embA 4245491 c.2259T>G synonymous_variant 0.25
embB 4245524 c.-990G>T upstream_gene_variant 0.29
embB 4247107 c.594C>A synonymous_variant 0.14
ethR 4327549 c.2delT frameshift_variant 0.13
ethR 4328126 p.Ser193* stop_gained 0.17
whiB6 4338302 p.Gly74Trp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0