TB-Profiler result

Run: ERR1949994
Summary

Run ID: ERR1949994

Sample name:

Date: 31-03-2023 15:36:52

Number of reads: 284811

Percentage reads mapped: 99.13

Strain: lineage4

Drug-resistance: MDR-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
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
rpoB 761136 p.Thr444Pro missense_variant 0.67 rifampicin
rpoB 761154 p.Ser450Ala missense_variant 0.5 rifampicin
katG 2155859 p.Thr85Pro missense_variant 0.67 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 5086 c.-154A>C upstream_gene_variant 0.4
gyrB 5686 c.447T>A synonymous_variant 0.6
gyrB 6314 p.Ser359Thr missense_variant 0.33
gyrB 6353 p.Lys372* stop_gained 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8075 p.Glu258Asp missense_variant 0.4
gyrA 8316 p.Thr339Pro missense_variant 0.29
gyrA 8404 p.His368Leu missense_variant 0.33
gyrA 9807 p.Thr836Ala missense_variant 0.18
mshA 575590 c.243T>C synonymous_variant 0.33
mshA 575604 p.Val86Ala missense_variant 0.22
mshA 575757 p.Leu137Arg missense_variant 0.25
ccsA 619943 p.Phe18Ser missense_variant 0.22
ccsA 620056 p.Thr56Pro missense_variant 0.5
ccsA 620117 p.Val76Gly missense_variant 0.75
rpoB 760770 p.Ile322Phe missense_variant 0.4
rpoB 761283 p.Ser493Ala missense_variant 0.22
rpoB 761398 p.Asp531Ala missense_variant 0.4
rpoB 761491 p.Val562Gly missense_variant 0.33
rpoC 763532 p.Thr55Pro missense_variant 0.5
rpoC 766283 p.Thr972Ala missense_variant 0.33
rpoC 766301 p.Cys978Ser missense_variant 0.29
rpoC 766442 p.Thr1025Pro missense_variant 0.25
rpoC 766712 p.Ser1115Ala missense_variant 0.25
rpoC 766865 p.Thr1166Pro missense_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775677 p.Lys935Met missense_variant 0.4
mmpL5 777354 p.Val376Gly missense_variant 0.22
mmpL5 777378 p.Leu368Arg missense_variant 0.27
mmpL5 778011 p.Gln157Leu missense_variant 0.29
mmpR5 778034 c.-956A>T upstream_gene_variant 0.29
mmpL5 778078 p.Thr135Pro missense_variant 0.29
mmpS5 778566 p.Cys114Ser missense_variant 0.33
mmpS5 778793 p.Leu38* stop_gained 0.3
mmpL5 778816 c.-336T>A upstream_gene_variant 0.25
rpsL 781365 c.-195T>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781512 c.-48A>T upstream_gene_variant 0.33
fbiC 1303525 p.Ser199Ala missense_variant 0.5
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304699 p.Glu590Ala missense_variant 0.25
fbiC 1305433 p.Ala835Ser missense_variant 0.25
embR 1416514 p.Asp278Glu missense_variant 0.5
embR 1416847 p.Val167Gly missense_variant 0.29
embR 1416925 c.423A>T synonymous_variant 0.4
atpE 1461285 p.Lys81* stop_gained 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471844 n.-2G>T upstream_gene_variant 0.25
rrs 1471862 n.17T>A non_coding_transcript_exon_variant 0.3
rrs 1472249 n.404T>G non_coding_transcript_exon_variant 0.22
rrs 1472528 n.683T>C non_coding_transcript_exon_variant 0.33
rrs 1473170 n.1325A>T non_coding_transcript_exon_variant 0.4
rrs 1473183 n.1338A>T non_coding_transcript_exon_variant 0.4
rrl 1473824 n.167A>T non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474017 n.360A>T non_coding_transcript_exon_variant 0.5
rrl 1474033 n.376A>T non_coding_transcript_exon_variant 0.5
rrl 1474298 n.641T>A non_coding_transcript_exon_variant 0.18
rrl 1474927 n.1270T>G non_coding_transcript_exon_variant 0.22
rrl 1476190 n.2533C>A non_coding_transcript_exon_variant 0.5
rrl 1476335 n.2678C>A non_coding_transcript_exon_variant 0.67
rpsA 1833406 c.-136A>T upstream_gene_variant 0.4
rpsA 1833506 c.-36C>A upstream_gene_variant 0.5
rpsA 1833988 c.447C>A synonymous_variant 0.33
rpsA 1834240 c.699T>G synonymous_variant 0.22
rpsA 1834308 p.Asp256Gly missense_variant 0.22
rpsA 1834791 p.Arg417Leu missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101718 p.Leu442Arg missense_variant 0.5
ndh 2101957 p.Phe362Leu missense_variant 0.4
katG 2154243 p.Glu623Asp missense_variant 0.67
katG 2154696 c.1416A>T synonymous_variant 0.4
katG 2155086 c.1026G>A synonymous_variant 1.0
katG 2155200 p.Tyr304* stop_gained 0.4
katG 2155521 p.Tyr197* stop_gained 0.4
katG 2155945 p.Asp56Ala missense_variant 0.29
katG 2156343 c.-232A>T upstream_gene_variant 0.67
PPE35 2168552 c.2061T>A synonymous_variant 0.33
PPE35 2168596 p.Phe673Ile missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169019 p.Leu532Met missense_variant 0.33
PPE35 2169104 c.1509G>A synonymous_variant 0.4
PPE35 2169379 p.Phe412Ile missense_variant 0.22
PPE35 2170432 p.Ser61Ala missense_variant 0.4
Rv1979c 2221922 p.Lys415* stop_gained 0.33
Rv1979c 2223013 p.Tyr51Phe missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288862 p.Glu127Val missense_variant 0.25
pncA 2288865 p.Asp126Val missense_variant 0.22
kasA 2518314 p.Pro67Gln missense_variant 0.67
kasA 2518607 p.Met165Leu missense_variant 0.33
kasA 2518625 p.Cys171Gly missense_variant 0.33
kasA 2518707 p.Val198Gly missense_variant 0.5
kasA 2519012 c.898T>C synonymous_variant 0.33
eis 2714312 p.Thr341Pro missense_variant 0.29
eis 2714884 p.His150Leu missense_variant 0.3
eis 2715086 p.Ser83Cys missense_variant 0.29
eis 2715103 p.Leu77Arg missense_variant 0.22
folC 2746262 p.Leu446Gln missense_variant 0.4
folC 2746285 p.Asp438Glu missense_variant 0.5
folC 2746485 p.Phe372Ile missense_variant 0.33
folC 2746551 p.Ile350Leu missense_variant 0.5
folC 2747442 c.157T>C synonymous_variant 1.0
folC 2747677 c.-79T>G upstream_gene_variant 0.33
pepQ 2859313 p.Leu369Gln missense_variant 0.29
pepQ 2859834 c.585T>G synonymous_variant 0.4
pepQ 2860114 p.Val102Gly missense_variant 0.29
pepQ 2860129 p.Phe97Cys missense_variant 0.33
ribD 2987192 c.354A>T synonymous_variant 0.29
ribD 2987453 c.615T>G synonymous_variant 0.5
Rv2752c 3065213 p.Thr327Ala missense_variant 0.33
Rv2752c 3065215 p.Ile326Ser missense_variant 0.4
Rv2752c 3066224 c.-33T>G upstream_gene_variant 0.5
Rv2752c 3067041 c.-850C>A upstream_gene_variant 0.5
thyX 3067249 p.Thr233Pro missense_variant 0.4
thyA 3073777 p.Leu232Gln missense_variant 0.29
ald 3087183 p.Thr122Pro missense_variant 0.38
ald 3087825 p.Asn336Asp missense_variant 0.33
fprA 3473837 c.-170A>T upstream_gene_variant 0.4
fprA 3474059 p.Ala18Gly missense_variant 0.33
fprA 3475151 p.Leu382* stop_gained 0.29
fprA 3475163 p.Leu386His missense_variant 0.29
whiB7 3568687 c.-8A>T upstream_gene_variant 0.5
Rv3236c 3612186 p.Phe311Ile missense_variant 0.67
Rv3236c 3612572 p.Val182Gly missense_variant 0.22
Rv3236c 3612605 p.Val171Gly missense_variant 0.4
Rv3236c 3612986 p.Gly44Val missense_variant 0.4
fbiA 3641021 p.Val160Asp missense_variant 0.33
fbiA 3641086 p.Thr182Pro missense_variant 0.29
fbiA 3641239 p.Leu233Val missense_variant 0.5
fbiB 3642062 p.Tyr176* stop_gained 0.22
fbiB 3642280 p.Leu249Arg missense_variant 0.5
alr 3840217 p.Tyr402Asn missense_variant 0.22
alr 3840408 p.Val338Ala missense_variant 0.17
alr 3840429 p.Asn331Thr missense_variant 0.29
alr 3840543 p.Val293Gly missense_variant 0.25
alr 3840588 p.Lys278Ile missense_variant 0.36
alr 3841269 p.Val51Ala missense_variant 0.17
alr 3841572 c.-152T>A upstream_gene_variant 0.4
rpoA 3878463 c.45C>A synonymous_variant 0.4
clpC1 4039121 c.1584T>G synonymous_variant 0.29
clpC1 4039335 p.Leu457Gln missense_variant 0.22
clpC1 4039498 p.Ile403Val missense_variant 0.21
clpC1 4039897 p.Lys270Glu missense_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040522 p.Ser61Arg missense_variant 0.5
clpC1 4040877 c.-173T>G upstream_gene_variant 0.25
clpC1 4040890 c.-186A>G upstream_gene_variant 0.33
embC 4240017 p.Val52Gly missense_variant 0.25
embC 4240069 p.Ser69Arg missense_variant 0.33
embC 4240712 p.Trp284Arg missense_variant 0.4
embC 4240979 p.Thr373Pro missense_variant 0.25
embC 4242468 p.Tyr869Cys missense_variant 0.22
embC 4242479 p.Thr873Ala missense_variant 0.44
embC 4242486 p.Glu875Ala missense_variant 0.43
embC 4242602 p.Ser914Ala missense_variant 0.33
embA 4242625 c.-608T>C upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243138 c.-95C>A upstream_gene_variant 0.22
embA 4243208 c.-25A>C upstream_gene_variant 0.25
embA 4243398 p.Thr56Pro missense_variant 0.33
embA 4243849 p.Val206Gly missense_variant 0.25
embA 4244608 p.Leu459Arg missense_variant 0.25
embA 4244880 p.Trp550Gly missense_variant 0.5
embA 4245949 p.Gln906Pro missense_variant 0.25
embB 4246911 p.Leu133* stop_gained 0.25
embB 4247141 p.Phe210Val missense_variant 0.5
embB 4247219 p.Leu236Val missense_variant 0.5
embB 4247742 p.Leu410Arg missense_variant 0.29
embB 4248395 p.Phe628Val missense_variant 0.44
embB 4248587 p.Gly692Ser missense_variant 0.29
aftB 4267685 c.1152T>G synonymous_variant 0.4
ubiA 4269988 c.-155T>A upstream_gene_variant 0.4
ethA 4327083 p.Cys131Ser missense_variant 0.6
ethA 4327127 p.Trp116Leu missense_variant 0.4
ethR 4327817 p.Leu90His missense_variant 0.5
ethR 4328058 p.Glu170Asp missense_variant 0.67
ethA 4328345 c.-872T>A upstream_gene_variant 0.29
ethA 4328352 c.-879T>C upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407552 c.651G>T synonymous_variant 0.5
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0