Run ID: ERR2514729
Sample name:
Date: 31-03-2023 20:31:33
Number of reads: 604094
Percentage reads mapped: 99.28
Strain: lineage3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin |
rpoB | 761108 | p.Met434Ile | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.95 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6763 | c.-539G>A | upstream_gene_variant | 0.14 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9461 | c.2160C>T | synonymous_variant | 0.14 |
gyrA | 9629 | c.2328C>T | synonymous_variant | 1.0 |
fgd1 | 490622 | c.-161G>T | upstream_gene_variant | 0.18 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 619995 | c.107delT | frameshift_variant | 0.17 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765706 | c.2337G>A | synonymous_variant | 0.12 |
rpoC | 765732 | p.Ala788Glu | missense_variant | 0.14 |
rpoC | 766490 | p.Arg1041Gly | missense_variant | 0.16 |
rpoC | 766582 | c.3213C>A | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777147 | p.Pro445His | missense_variant | 0.12 |
mmpL5 | 777157 | p.Arg442Trp | missense_variant | 0.13 |
mmpL5 | 778624 | c.-144C>T | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406696 | c.645G>T | synonymous_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674742 | p.Lys181Glu | missense_variant | 0.14 |
inhA | 1674858 | c.657G>A | synonymous_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102605 | c.438G>A | synonymous_variant | 0.14 |
katG | 2154120 | p.Met664Ile | missense_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2156096 | p.Pro6Ser | missense_variant | 0.12 |
PPE35 | 2167707 | p.Gly969Asp | missense_variant | 0.11 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.96 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
eis | 2715347 | c.-15C>T | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
folC | 2746653 | p.Gly316Ser | missense_variant | 0.12 |
Rv2752c | 3064698 | c.1494C>G | synonymous_variant | 0.13 |
Rv2752c | 3065069 | p.His375Tyr | missense_variant | 1.0 |
Rv2752c | 3065224 | p.His323Leu | missense_variant | 0.12 |
Rv2752c | 3067080 | c.-890_-889delTGinsCC | upstream_gene_variant | 0.12 |
thyX | 3067922 | c.24C>T | synonymous_variant | 0.14 |
thyA | 3074298 | p.Glu58Asp | missense_variant | 0.13 |
thyA | 3074578 | c.-107C>T | upstream_gene_variant | 0.13 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087837 | p.Ala340Thr | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>T | synonymous_variant | 0.11 |
whiB7 | 3568702 | c.-23C>A | upstream_gene_variant | 1.0 |
fbiB | 3641517 | c.-18C>T | upstream_gene_variant | 0.12 |
alr | 3840937 | c.484C>T | synonymous_variant | 0.12 |
alr | 3841473 | c.-53G>A | upstream_gene_variant | 1.0 |
embC | 4240388 | p.Asn176His | missense_variant | 1.0 |
embC | 4241175 | p.Ser438Tyr | missense_variant | 0.12 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242706 | p.Asp948Glu | missense_variant | 0.12 |
embC | 4242776 | p.Gln972Lys | missense_variant | 0.12 |
aftB | 4268114 | c.723G>T | synonymous_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4408012 | c.190dupC | frameshift_variant | 0.93 |