TB-Profiler result

Run: ERR3077931
Summary

Run ID: ERR3077931

Sample name:

Date: 01-04-2023 00:11:16

Number of reads: 550936

Percentage reads mapped: 99.55

Strain: lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.53 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289096 p.Asp49Gly missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9057 p.Glu586Gln missense_variant 0.17
gyrA 9072 p.Ala591Ser missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490811 p.Ala10Glu missense_variant 0.2
fgd1 490934 p.Ala51Asp missense_variant 0.12
mshA 575296 c.-51delG upstream_gene_variant 0.22
mshA 575649 p.Val101Ala missense_variant 0.17
mshA 575677 c.330C>G synonymous_variant 0.15
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576299 p.Glu318Lys missense_variant 0.2
ccsA 619796 c.-95G>A upstream_gene_variant 0.14
ccsA 620425 p.Val179Leu missense_variant 0.29
ccsA 620537 p.Val216Glu missense_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759950 c.144T>A synonymous_variant 0.18
rpoB 759980 c.174G>T synonymous_variant 0.15
rpoB 760035 p.Val77Leu missense_variant 0.14
rpoB 760050 p.Glu82* stop_gained 0.12
rpoB 760223 c.417T>C synonymous_variant 0.12
rpoB 761039 p.Leu411Phe missense_variant 0.29
rpoB 761364 p.Asp520Asn missense_variant 0.17
rpoB 761373 p.Val523Met missense_variant 0.14
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 762352 p.Arg849Pro missense_variant 0.22
rpoB 762355 p.Glu850Gly missense_variant 0.22
rpoB 762763 p.Thr986Met missense_variant 0.2
rpoC 763324 c.-46A>G upstream_gene_variant 0.1
rpoC 764512 c.1143G>T synonymous_variant 0.15
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765083 p.Arg572Cys missense_variant 0.25
rpoC 765620 p.Glu751* stop_gained 0.15
rpoC 765687 p.Ala773Glu missense_variant 0.14
rpoC 765787 c.2418C>T synonymous_variant 0.12
rpoC 765820 c.2451G>T synonymous_variant 0.12
rpoC 766219 p.Asp950Glu missense_variant 0.18
rpoC 767281 c.3912C>G synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776226 c.2253_2254delGG frameshift_variant 0.12
mmpS5 778749 p.Pro53Ser missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781704 p.Leu49Ile missense_variant 0.22
rplC 801003 c.195G>A synonymous_variant 0.2
rplC 801366 c.558_559insC frameshift_variant 0.2
fbiC 1304028 p.Asn366Lys missense_variant 0.22
fbiC 1305444 c.2514A>G synonymous_variant 0.29
Rv1258c 1407312 p.Phe10Tyr missense_variant 0.13
embR 1416383 p.Ser322Ile missense_variant 0.11
embR 1416606 p.Arg248Cys missense_variant 0.12
atpE 1461257 p.Met71Ile missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471679 n.-167C>A upstream_gene_variant 0.15
rrs 1472194 n.349G>T non_coding_transcript_exon_variant 0.25
rrs 1472476 n.631A>G non_coding_transcript_exon_variant 0.15
rrs 1472736 n.891G>T non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.15
rrs 1473342 n.1497G>A non_coding_transcript_exon_variant 0.12
rrl 1474526 n.869C>A non_coding_transcript_exon_variant 0.29
rrl 1474840 n.1183A>G non_coding_transcript_exon_variant 0.11
rrl 1475173 n.1516A>G non_coding_transcript_exon_variant 0.17
rrl 1475287 n.1630G>T non_coding_transcript_exon_variant 0.11
rrl 1476448 n.2791G>T non_coding_transcript_exon_variant 0.67
rrl 1476666 n.3009C>A non_coding_transcript_exon_variant 0.25
fabG1 1673444 p.Thr2Asn missense_variant 0.13
inhA 1674622 p.Gly141* stop_gained 0.12
rpsA 1833635 p.Tyr32His missense_variant 0.14
rpsA 1833822 p.Glu94Gly missense_variant 0.12
rpsA 1834465 c.924T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918496 p.Glu186Val missense_variant 0.18
tlyA 1918499 p.Val187Ala missense_variant 0.18
ndh 2101807 c.1236C>A synonymous_variant 0.12
ndh 2102195 p.Ser283Ile missense_variant 0.2
ndh 2102711 p.Pro111His missense_variant 0.2
ndh 2102845 c.198A>G synonymous_variant 0.17
katG 2154776 p.Ser446Gly missense_variant 0.25
katG 2156140 c.-29C>A upstream_gene_variant 0.17
katG 2156147 c.-36C>A upstream_gene_variant 0.14
PPE35 2168195 c.2418G>T synonymous_variant 0.12
PPE35 2168249 p.Gln788His missense_variant 0.13
PPE35 2168597 c.2016A>G synonymous_variant 0.25
PPE35 2168787 p.Thr609Lys missense_variant 0.12
PPE35 2168974 p.Asn547His missense_variant 0.15
PPE35 2169615 p.Asn333Ile missense_variant 0.2
PPE35 2170159 p.Ala152Thr missense_variant 0.22
PPE35 2170352 c.261C>T synonymous_variant 0.18
Rv1979c 2221957 p.Glu403Gly missense_variant 0.15
Rv1979c 2222239 p.Leu309Arg missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289380 c.-139G>T upstream_gene_variant 0.2
pncA 2289642 c.-401A>G upstream_gene_variant 0.13
kasA 2518589 p.Gly159Trp missense_variant 0.14
kasA 2518672 c.558G>T synonymous_variant 0.17
kasA 2518701 p.Gly196Asp missense_variant 0.15
eis 2714349 c.984G>T synonymous_variant 0.13
eis 2715274 p.Ala20Val missense_variant 0.18
eis 2715419 c.-88_-87insG upstream_gene_variant 0.18
ahpC 2726639 c.447C>A synonymous_variant 0.17
folC 2747126 p.Met158Thr missense_variant 0.2
folC 2747515 c.84G>C synonymous_variant 0.12
folC 2747528 p.Ile24Thr missense_variant 0.1
pepQ 2859872 p.His183Asn missense_variant 0.22
Rv2752c 3065502 p.Asp230Glu missense_variant 0.25
Rv2752c 3066130 p.Leu21Pro missense_variant 0.17
Rv2752c 3066205 c.-14A>G upstream_gene_variant 0.5
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067264 p.Ala228Ser missense_variant 0.15
thyX 3067424 c.522G>T synonymous_variant 0.2
thyX 3067892 c.54G>A synonymous_variant 0.15
thyA 3074430 c.42G>T synonymous_variant 0.22
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087241 p.Ala141Asp missense_variant 0.14
ald 3087621 p.Ala268Thr missense_variant 0.11
ald 3087643 p.Phe275Ser missense_variant 0.11
fbiD 3339150 c.33C>A synonymous_variant 0.25
Rv3083 3448976 p.Arg158Leu missense_variant 0.29
Rv3083 3449483 c.983dupG frameshift_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474217 p.Ala71Pro missense_variant 0.17
fprA 3474511 p.Asp169Tyr missense_variant 0.18
fprA 3474660 c.654C>A synonymous_variant 0.4
whiB7 3568436 p.Pro82Thr missense_variant 0.14
whiB7 3568616 p.Val22Phe missense_variant 0.14
Rv3236c 3612348 p.Asp257Tyr missense_variant 0.18
Rv3236c 3612384 p.Phe245Val missense_variant 0.2
Rv3236c 3612577 c.540G>A synonymous_variant 0.2
Rv3236c 3612701 p.Asp139Val missense_variant 1.0
Rv3236c 3612915 p.Leu68Val missense_variant 0.12
fbiA 3640586 p.Phe15Tyr missense_variant 0.25
fbiA 3640720 c.178_179insT frameshift_variant 0.33
fbiA 3641248 p.Ala236Ser missense_variant 0.18
fbiB 3641557 p.Ser8Phe missense_variant 0.14
fbiB 3641755 p.Arg74Leu missense_variant 0.17
fbiB 3641971 p.Val146Ala missense_variant 0.2
fbiB 3642014 p.Gln160His missense_variant 0.2
fbiB 3642025 p.Ala164Glu missense_variant 0.2
fbiB 3642386 c.852C>A synonymous_variant 0.14
alr 3840413 c.1008C>A synonymous_variant 0.15
alr 3840988 p.Val145Leu missense_variant 0.17
alr 3841352 p.Leu23Phe missense_variant 0.18
alr 3841379 c.42G>A synonymous_variant 0.13
rpoA 3877972 p.Asp179Ala missense_variant 0.1
ddn 3987160 p.Val106Ala missense_variant 0.21
clpC1 4039011 p.Ala565Gly missense_variant 0.12
clpC1 4039262 c.1443C>T synonymous_variant 0.18
clpC1 4039737 p.Thr323Asn missense_variant 0.17
clpC1 4040241 p.Thr155Phe missense_variant 0.17
clpC1 4040249 p.Glu152Gly missense_variant 0.17
clpC1 4040890 c.-186A>G upstream_gene_variant 0.15
embC 4240648 c.786C>T synonymous_variant 0.25
embC 4240715 p.His285Asn missense_variant 0.25
embC 4240797 p.Asn312Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267142 c.1695C>T synonymous_variant 0.18
aftB 4267158 p.Thr560Lys missense_variant 0.18
aftB 4267871 p.Gln322His missense_variant 0.25
aftB 4268133 p.Leu235Pro missense_variant 0.15
aftB 4268136 p.Leu234Pro missense_variant 0.17
aftB 4268548 p.Leu97Met missense_variant 0.17
ubiA 4269200 p.Ser212Gly missense_variant 0.12
ethA 4326009 p.Val489Phe missense_variant 0.12
ethA 4326660 p.Leu272Ile missense_variant 0.22
ethA 4326810 p.Ala222Ser missense_variant 0.18
ethA 4326812 p.Ile221Thr missense_variant 0.18
ethA 4327421 p.Ser18Ile missense_variant 0.12
ethR 4327798 p.Asp84Tyr missense_variant 0.22
whiB6 4338355 p.Cys56Tyr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407834 p.Trp123Cys missense_variant 0.22
gid 4407954 c.249G>A synonymous_variant 0.14
gid 4408171 p.Ile11Thr missense_variant 0.14
gid 4408202 c.1A>G start_lost 0.13
gid 4408208 c.-6T>C upstream_gene_variant 0.13
gid 4408354 c.-152G>A upstream_gene_variant 0.11