Run ID: SRR6045206
Sample name:
Date: 04-04-2023 11:54:43
Number of reads: 599379
Percentage reads mapped: 48.73
Strain: lineage1.2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 1.0 |
lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491554 | p.Gln258* | stop_gained | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 760434 | p.Val210Ile | missense_variant | 0.13 |
rpoB | 761837 | p.Cys677* | stop_gained | 0.12 |
rpoC | 762737 | c.-633C>T | upstream_gene_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764080 | c.711C>T | synonymous_variant | 0.13 |
rpoC | 766954 | c.3585C>T | synonymous_variant | 0.14 |
rpoC | 766969 | c.3600C>T | synonymous_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777623 | p.Gln286His | missense_variant | 0.12 |
mmpL5 | 778612 | c.-132C>T | upstream_gene_variant | 0.12 |
rpsL | 781385 | c.-175C>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407527 | c.-187G>A | upstream_gene_variant | 0.15 |
embR | 1416713 | p.Ile212Thr | missense_variant | 0.1 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473401 | n.-257G>A | upstream_gene_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168031 | p.Thr861Lys | missense_variant | 0.11 |
PPE35 | 2168205 | p.Pro803Gln | missense_variant | 1.0 |
PPE35 | 2168775 | p.Pro613Leu | missense_variant | 0.13 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289358 | c.-117T>G | upstream_gene_variant | 0.17 |
pncA | 2289468 | c.-227G>T | upstream_gene_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2519217 | p.Pro368Leu | missense_variant | 0.22 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
pepQ | 2859886 | p.Ala178Asp | missense_variant | 0.15 |
Rv2752c | 3065165 | p.Gly343Ser | missense_variant | 0.12 |
Rv2752c | 3066301 | c.-111dupC | upstream_gene_variant | 0.1 |
Rv2752c | 3067032 | c.-841C>A | upstream_gene_variant | 0.12 |
thyX | 3067238 | c.708C>T | synonymous_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086929 | p.Ala37Val | missense_variant | 0.15 |
Rv3083 | 3448700 | p.Phe66Ser | missense_variant | 0.12 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3474653 | p.Ala216Val | missense_variant | 0.13 |
fprA | 3474911 | p.Val302Ala | missense_variant | 0.17 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
Rv3236c | 3612804 | p.Ala105Thr | missense_variant | 1.0 |
fbiA | 3640579 | p.Ala13Thr | missense_variant | 0.12 |
fbiB | 3642785 | c.1251C>T | synonymous_variant | 0.15 |
fbiB | 3642800 | c.1266C>T | synonymous_variant | 0.13 |
rpoA | 3878483 | c.25C>T | synonymous_variant | 0.12 |
rpoA | 3878561 | c.-54C>T | upstream_gene_variant | 0.5 |
ddn | 3987184 | p.Ala114Val | missense_variant | 0.11 |
clpC1 | 4039062 | p.Ser548Leu | missense_variant | 0.17 |
clpC1 | 4039654 | p.Thr351Ser | missense_variant | 0.14 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4044307 | c.-26A>G | upstream_gene_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4240750 | c.888C>T | synonymous_variant | 1.0 |
embC | 4241022 | p.Ala387Val | missense_variant | 0.12 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242653 | p.Ala931Thr | missense_variant | 0.14 |
embC | 4242671 | p.Pro937Ser | missense_variant | 0.15 |
embA | 4243474 | p.Thr81Met | missense_variant | 0.12 |
embA | 4243532 | c.300C>A | synonymous_variant | 1.0 |
embA | 4243539 | p.Ala103Thr | missense_variant | 0.13 |
embA | 4243721 | c.489G>A | synonymous_variant | 0.13 |
embA | 4244282 | c.1050C>A | synonymous_variant | 0.15 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246275 | p.Ala1015Thr | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248343 | c.1830G>T | synonymous_variant | 0.13 |
embB | 4249330 | p.Met939Ile | missense_variant | 0.27 |
aftB | 4267835 | p.Met334Ile | missense_variant | 0.15 |
aftB | 4268614 | p.Gly75Arg | missense_variant | 0.18 |
aftB | 4268630 | p.Val69Ile | missense_variant | 0.14 |
aftB | 4268811 | p.Ser9Leu | missense_variant | 0.11 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
ubiA | 4269469 | p.Pro122Gln | missense_variant | 0.94 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4408124 | p.Ala27Pro | missense_variant | 1.0 |