TB-Profiler result

Run: ERR5908173

Summary

Run ID: ERR5908173

Sample name:

Date: 02-04-2023 00:52:02

Number of reads: 772508

Percentage reads mapped: 99.67

Strain: lineage4.3.3

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrB 6749 p.Ala504Thr missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155030 p.Ala361Asp missense_variant 0.14 isoniazid
ethA 4326880 c.593delG frameshift_variant 0.11 ethionamide
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 6634 c.-668T>C upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7562 c.261C>T synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8435 c.1134C>T synonymous_variant 0.12
gyrA 8527 p.Arg409Leu missense_variant 0.12
gyrA 9046 p.Tyr582Phe missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490782 c.-1G>C upstream_gene_variant 0.11
mshA 575282 c.-66C>T upstream_gene_variant 0.2
mshA 575514 p.Pro56Leu missense_variant 0.15
mshA 576483 p.Val379Ala missense_variant 0.29
ccsA 620253 c.363G>A synonymous_variant 0.15
rpoB 759824 p.Gln6His missense_variant 0.12
rpoB 760508 c.702G>T synonymous_variant 0.13
rpoB 761720 c.1914C>G synonymous_variant 0.22
rpoB 761993 c.2187C>T synonymous_variant 0.12
rpoB 762178 p.Arg791His missense_variant 0.17
rpoB 763057 p.Thr1084Ile missense_variant 0.13
rpoC 763510 c.141C>T synonymous_variant 0.11
rpoC 764410 c.1041G>T synonymous_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766096 c.2727G>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776887 p.Asn532Asp missense_variant 0.11
mmpL5 777389 p.Phe364Leu missense_variant 0.13
mmpL5 778663 c.-183C>T upstream_gene_variant 0.15
mmpS5 778902 p.Ile2Val missense_variant 0.1
mmpL5 778960 c.-480G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800720 c.-88delC upstream_gene_variant 0.11
fbiC 1303930 p.Pro334Thr missense_variant 0.11
fbiC 1304716 p.Ala596Ser missense_variant 0.2
fbiC 1305202 p.Arg758Gly missense_variant 0.1
Rv1258c 1406276 c.1065G>A synonymous_variant 0.13
Rv1258c 1406299 p.Val348Leu missense_variant 0.15
Rv1258c 1406643 p.Leu233Pro missense_variant 0.12
embR 1416480 p.Ala290Thr missense_variant 0.15
atpE 1460985 c.-59delA upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471689 n.-157T>C upstream_gene_variant 0.17
rrs 1472019 n.174G>T non_coding_transcript_exon_variant 0.67
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.14
rrs 1473312 n.1467G>T non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>C non_coding_transcript_exon_variant 1.0
inhA 1674276 p.Ile25Met missense_variant 0.12
inhA 1674874 p.Arg225Ser missense_variant 0.11
rpsA 1833438 c.-104C>G upstream_gene_variant 0.14
rpsA 1833726 p.Val62Ala missense_variant 0.12
rpsA 1834448 p.Lys303Glu missense_variant 0.15
rpsA 1834836 p.Met432Thr missense_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102058 p.Val329Met missense_variant 0.13
ndh 2102080 c.963C>T synonymous_variant 0.13
ndh 2102092 c.951G>T synonymous_variant 0.14
ndh 2102119 c.924C>T synonymous_variant 0.14
ndh 2102499 p.Gly182Arg missense_variant 0.2
katG 2154536 p.Glu526Lys missense_variant 0.11
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156418 c.-307G>T upstream_gene_variant 0.22
PPE35 2168342 c.2271T>A synonymous_variant 0.2
PPE35 2169253 p.Ala454Ser missense_variant 0.29
PPE35 2169522 p.Ala364Glu missense_variant 0.18
PPE35 2169692 c.921C>A synonymous_variant 0.12
PPE35 2169750 p.Gly288Val missense_variant 0.12
PPE35 2170292 c.321G>A synonymous_variant 0.13
PPE35 2170445 c.168G>T synonymous_variant 0.15
PPE35 2170498 p.Ala39Ser missense_variant 0.17
Rv1979c 2221962 c.1203A>T synonymous_variant 0.12
Rv1979c 2222778 c.387C>T synonymous_variant 0.13
Rv1979c 2222991 c.174G>T synonymous_variant 0.13
Rv1979c 2223156 p.Gly3Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288719 p.Met175Leu missense_variant 0.11
pncA 2288725 p.Glu173Lys missense_variant 0.11
pncA 2289951 c.-710G>T upstream_gene_variant 0.21
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714376 c.957G>T synonymous_variant 0.22
eis 2714858 p.Gly159Cys missense_variant 0.2
ahpC 2726281 p.Gln30Arg missense_variant 0.2
ahpC 2726536 p.Lys115Arg missense_variant 0.15
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747194 p.Asp135Glu missense_variant 0.11
folC 2747292 p.Ser103Thr missense_variant 0.18
folC 2747727 c.-129C>A upstream_gene_variant 0.11
pepQ 2860254 c.165C>A synonymous_variant 0.14
ribD 2987158 p.Gln107Arg missense_variant 0.25
Rv2752c 3066110 p.Gly28Cys missense_variant 0.17
thyX 3067210 c.736T>C synonymous_variant 0.11
thyX 3067312 p.Ala212Thr missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086796 c.-24C>A upstream_gene_variant 0.13
ald 3087424 p.Asp202Val missense_variant 0.11
ald 3087444 p.Ala209Ser missense_variant 0.12
fbiD 3339087 c.-31C>A upstream_gene_variant 0.17
fbiD 3339135 p.Asp6Glu missense_variant 0.18
fbiD 3339263 p.Ala49Val missense_variant 0.13
fbiD 3339308 p.Pro64Leu missense_variant 0.12
Rv3083 3448514 p.His4Arg missense_variant 0.11
Rv3083 3448586 p.Pro28His missense_variant 0.12
Rv3083 3449946 c.1443C>T synonymous_variant 0.11
fprA 3473946 c.-61T>C upstream_gene_variant 0.15
fprA 3473960 c.-47T>C upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475207 p.Asp401Tyr missense_variant 0.12
Rv3236c 3613201 c.-85C>T upstream_gene_variant 0.12
fbiA 3640424 c.-118delT upstream_gene_variant 0.12
fbiB 3642194 p.Phe220Leu missense_variant 0.18
alr 3840431 c.990C>A synonymous_variant 0.12
alr 3840882 p.Arg180Leu missense_variant 0.2
alr 3841014 p.Arg136Pro missense_variant 0.11
rpoA 3878495 p.Gln5* stop_gained 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039804 p.Ala301Ser missense_variant 0.14
clpC1 4040587 p.Glu40* stop_gained 0.22
embC 4239950 c.88C>A synonymous_variant 0.12
embC 4240324 c.462G>T synonymous_variant 0.13
embC 4240546 c.684G>T synonymous_variant 0.13
embC 4241198 p.Ile446Val missense_variant 0.12
embC 4241650 p.Leu596Phe missense_variant 0.13
embC 4242323 p.Gly821Ser missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243099 c.-134G>A upstream_gene_variant 0.22
embA 4243853 p.Met207Ile missense_variant 0.33
embA 4244116 p.Arg295Gln missense_variant 0.17
embA 4244166 p.Ala312Thr missense_variant 0.14
embA 4244874 p.Pro548Ser missense_variant 0.67
embB 4247022 p.Ala170Gly missense_variant 0.25
embB 4247976 p.Val488Asp missense_variant 0.1
embB 4249364 p.Glu951* stop_gained 0.13
aftB 4267688 c.1149G>A synonymous_variant 0.13
aftB 4268198 c.639C>A synonymous_variant 0.12
ethA 4326242 p.Asp411Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407851 p.Arg118Cys missense_variant 0.12
gid 4408000 p.Ile68Asn missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408254 c.-52G>T upstream_gene_variant 0.15