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
Drug | Resistance | Supporting mutations |
---|
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 |
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 |
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 |