TB-Profiler result

Run: ERR2228804
Summary

Run ID: ERR2228804

Sample name:

Date: 31-03-2023 16:21:31

Number of reads: 414924

Percentage reads mapped: 99.42

Strain: lineage4.8

Drug-resistance: RR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761114 p.Gln436His missense_variant 0.2 rifampicin
pncA 2289050 p.Tyr64* stop_gained 0.4 pyrazinamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7957 p.Val219Gly missense_variant 0.33
gyrA 9519 p.Tyr740Asn missense_variant 0.25
gyrA 9561 p.Met754Leu missense_variant 0.17
mshA 576237 p.Val297Ala missense_variant 0.18
ccsA 619884 c.-7A>G upstream_gene_variant 0.29
rpoB 760650 p.Thr282Pro missense_variant 0.2
rpoB 762214 p.Lys803Met missense_variant 0.4
rpoB 762276 p.Arg824Ser missense_variant 0.25
rpoC 765057 p.Asn563Ile missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776625 p.Asn619Thr missense_variant 0.2
mmpL5 777250 p.Tyr411Asp missense_variant 0.2
mmpL5 777369 p.Lys371Thr missense_variant 0.4
mmpL5 777988 p.Ser165Thr missense_variant 0.4
mmpL5 777999 p.Leu161Gln missense_variant 0.29
mmpL5 778412 p.Phe23Leu missense_variant 0.33
mmpR5 779066 p.Tyr26Phe missense_variant 0.5
mmpR5 779330 p.Leu114Gln missense_variant 0.33
rpsL 781371 c.-189T>G upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781918 p.Lys120Met missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303803 c.873C>A synonymous_variant 0.22
fbiC 1304971 p.Thr681Pro missense_variant 0.5
fbiC 1305033 c.2103T>G synonymous_variant 0.62
fbiC 1305040 p.Ser704Ala missense_variant 0.44
Rv1258c 1406748 p.Lys198Thr missense_variant 0.3
embR 1416547 p.Lys267Asn missense_variant 0.33
embR 1416584 p.Leu255Gln missense_variant 0.25
embR 1416608 p.Leu247* stop_gained 0.4
atpE 1461133 p.Val30Gly missense_variant 0.5
atpE 1461243 p.Asn67Tyr missense_variant 0.4
rrs 1471654 n.-192A>T upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471708 n.-138A>T upstream_gene_variant 0.38
rrs 1471716 n.-130T>A upstream_gene_variant 0.33
rrs 1473004 n.1159T>G non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474247 n.590A>T non_coding_transcript_exon_variant 0.4
rrl 1474450 n.793T>G non_coding_transcript_exon_variant 0.22
rrl 1474532 n.875T>G non_coding_transcript_exon_variant 0.5
rrl 1475823 n.2166A>T non_coding_transcript_exon_variant 0.25
rrl 1476679 n.3022T>A non_coding_transcript_exon_variant 0.4
fabG1 1673258 c.-182A>C upstream_gene_variant 0.25
fabG1 1673645 p.Asp69Val missense_variant 0.5
fabG1 1674050 p.Gln204Leu missense_variant 0.25
inhA 1674395 p.Val65Ala missense_variant 0.33
rpsA 1833944 p.Lys135* stop_gained 0.25
rpsA 1834179 p.Lys213Met missense_variant 0.29
rpsA 1834578 p.Val346Gly missense_variant 0.22
rpsA 1834614 p.Ile358Ser missense_variant 0.3
rpsA 1834676 p.Gly379Cys missense_variant 0.29
rpsA 1834941 p.Asp467Ala missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918105 p.Thr56Pro missense_variant 0.22
tlyA 1918221 c.282T>G synonymous_variant 0.3
tlyA 1918607 p.Val223Gly missense_variant 0.3
tlyA 1918704 c.765A>T synonymous_variant 0.33
ndh 2102721 p.Tyr108Asn missense_variant 0.5
katG 2155097 p.Tyr339Asn missense_variant 0.33
katG 2155760 p.Gly118Cys missense_variant 0.38
katG 2155785 c.327T>G synonymous_variant 0.29
katG 2156533 c.-422A>C upstream_gene_variant 0.43
PPE35 2168710 p.Asn635Tyr missense_variant 0.5
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168810 c.1803T>A synonymous_variant 0.6
PPE35 2168876 p.Phe579Leu missense_variant 0.5
PPE35 2170066 p.Ala183Thr missense_variant 0.25
PPE35 2170738 c.-126A>T upstream_gene_variant 0.25
Rv1979c 2222377 p.Val263Asp missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288841 p.Ala134Asp missense_variant 0.17
pncA 2288880 p.Arg121Leu missense_variant 0.18
pncA 2289376 c.-135T>G upstream_gene_variant 0.33
pncA 2289389 c.-148A>T upstream_gene_variant 0.29
pncA 2289553 c.-312C>A upstream_gene_variant 0.67
pncA 2289594 c.-353C>A upstream_gene_variant 0.29
pncA 2289782 c.-541A>C upstream_gene_variant 0.75
pncA 2290226 c.-985T>G upstream_gene_variant 0.5
kasA 2518203 p.Glu30Val missense_variant 0.5
kasA 2518663 c.549T>G synonymous_variant 0.22
kasA 2519352 p.Phe413Cys missense_variant 0.29
eis 2714391 c.942T>C synonymous_variant 0.13
eis 2714562 c.771T>A synonymous_variant 0.29
eis 2715095 p.Ala80Ser missense_variant 0.33
eis 2715574 c.-242T>C upstream_gene_variant 0.25
ahpC 2726400 p.Lys70* stop_gained 0.67
folC 2746377 p.Ser408Ala missense_variant 0.4
folC 2746769 p.Leu277Gln missense_variant 0.2
pepQ 2859629 p.Leu264Val missense_variant 0.43
ribD 2987263 p.Val142Gly missense_variant 0.25
Rv2752c 3064680 c.1512C>A synonymous_variant 0.33
Rv2752c 3065541 p.Glu217Asp missense_variant 0.5
thyA 3074089 p.Ile128Thr missense_variant 0.22
thyA 3074278 p.Gly65Val missense_variant 0.29
thyA 3074318 p.Phe52Ile missense_variant 0.33
thyA 3074334 c.138T>A synonymous_variant 0.43
ald 3087277 p.Gln153Leu missense_variant 0.29
ald 3087906 p.Phe363Val missense_variant 0.5
fbiD 3339633 c.516T>G synonymous_variant 0.29
fprA 3474142 p.Trp46Arg missense_variant 0.29
fprA 3475374 c.1368C>A synonymous_variant 0.33
Rv3236c 3612099 p.Ile340Phe missense_variant 0.29
Rv3236c 3613055 p.Leu21Arg missense_variant 0.2
Rv3236c 3613283 c.-167T>C upstream_gene_variant 0.22
fbiA 3640463 c.-80T>A upstream_gene_variant 0.38
fbiB 3642072 p.Arg180Ser missense_variant 0.25
fbiB 3642201 p.Ser223Ala missense_variant 0.18
fbiB 3642335 p.Ser267Arg missense_variant 0.2
fbiB 3642717 p.Ser395Cys missense_variant 0.43
alr 3840408 p.Val338Gly missense_variant 0.33
alr 3841095 p.Val109Gly missense_variant 0.29
alr 3841179 p.Ala81Asp missense_variant 0.22
alr 3841183 p.Thr80Pro missense_variant 0.3
alr 3841184 p.Gln79His missense_variant 0.2
rpoA 3877852 p.Phe219Ser missense_variant 0.29
rpoA 3878171 p.Pro113Ser missense_variant 0.22
ddn 3986655 c.-189A>G upstream_gene_variant 0.36
clpC1 4038306 p.Val800Gly missense_variant 0.33
clpC1 4038334 p.Phe791Ile missense_variant 0.22
clpC1 4038526 p.Ile727Leu missense_variant 0.4
clpC1 4038543 p.Gln721Pro missense_variant 0.33
clpC1 4039054 p.Phe551Ile missense_variant 0.33
clpC1 4039714 p.Tyr331Asn missense_variant 0.2
clpC1 4040409 p.Gly99Val missense_variant 0.33
embC 4240461 p.Val200Gly missense_variant 0.36
embC 4240581 p.Leu240Arg missense_variant 0.3
embC 4241593 c.1731C>A synonymous_variant 0.25
embC 4241685 p.Val608Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245121 p.Tyr630Phe missense_variant 0.4
embA 4246329 p.Thr1033Pro missense_variant 0.33
embB 4246841 p.Asn110Tyr missense_variant 0.31
embB 4247897 p.Met462Leu missense_variant 0.22
embB 4247945 p.Leu478Val missense_variant 0.3
embB 4248772 c.2259A>C synonymous_variant 0.22
embB 4249277 p.Tyr922His missense_variant 0.18
aftB 4267194 p.Pro548Gln missense_variant 0.14
aftB 4267242 p.Leu532Gln missense_variant 0.18
aftB 4267386 p.His484Arg missense_variant 0.33
aftB 4267597 p.Tyr414Asn missense_variant 0.25
aftB 4268799 p.Val13Gly missense_variant 0.3
ubiA 4269329 p.Lys169* stop_gained 0.22
ubiA 4269367 p.Ala156Gly missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethA 4327537 c.-64A>T upstream_gene_variant 0.4
ethR 4328060 p.Leu171Gln missense_variant 0.33
whiB6 4338223 p.Glu100Ala missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408119 c.84A>G synonymous_variant 0.43