Run ID: SRR17856659
Sample name:
Date: 03-04-2023 18:22:55
Number of reads: 5560314
Percentage reads mapped: 99.57
Strain: lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.25 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.13 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.18 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.18 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.13 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.3 |
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 | 764616 | p.Asn416Thr | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303331 | p.Arg134Leu | missense_variant | 0.16 |
embR | 1417517 | c.-170T>G | upstream_gene_variant | 0.24 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154692 | p.Ser474Ala | missense_variant | 0.18 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155685 | p.Lys143Glu | missense_variant | 0.84 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.23 |
PPE35 | 2169044 | c.1569G>C | synonymous_variant | 0.38 |
PPE35 | 2169047 | p.Ile522Val | missense_variant | 0.37 |
PPE35 | 2169053 | c.1560T>C | synonymous_variant | 0.61 |
PPE35 | 2169056 | c.1557A>G | synonymous_variant | 0.35 |
PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.25 |
PPE35 | 2169063 | p.Met517Thr | missense_variant | 0.62 |
PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.25 |
PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.25 |
PPE35 | 2169071 | c.1542A>G | synonymous_variant | 0.34 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.84 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
Rv2752c | 3064784 | p.Ser470Pro | missense_variant | 0.86 |
ald | 3086787 | c.-33A>C | upstream_gene_variant | 0.37 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473820 | c.-187C>A | upstream_gene_variant | 0.86 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fbiB | 3642877 | p.Lys448Arg | missense_variant | 0.19 |
embC | 4240009 | c.147G>A | synonymous_variant | 0.83 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4326848 | p.Pro209Leu | missense_variant | 0.18 |
whiB6 | 4338358 | p.Ala55Asp | missense_variant | 0.83 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407919 | c.259_283delCAGGTAGTTCTCCTAGAACCGCTAC | frameshift_variant | 0.75 |
gid | 4407985 | p.Gly73Glu | missense_variant | 0.75 |