Run ID: ERR4553549
Sample name:
Date: 01-04-2023 06:13:09
Number of reads: 1110903
Percentage reads mapped: 99.64
Strain: lineage3.1.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.98 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.99 |
lineage3.1.2.1 | East-African-Indian | CAS2 | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288826 | p.Val139Gly | missense_variant | 0.46 | pyrazinamide |
pncA | 2289172 | c.63_69dupAACCGGT | frameshift_variant | 0.25 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.33 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5945 | p.Arg236Cys | missense_variant | 0.16 |
gyrB | 6416 | p.Thr393Pro | missense_variant | 0.23 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.97 |
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 |
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 |
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.97 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288961 | p.Phe94Tyr | missense_variant | 0.17 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726115 | c.-77_-74delTTTG | upstream_gene_variant | 0.25 |
Rv2752c | 3064873 | p.Gly440Val | missense_variant | 0.1 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3841094 | c.327G>A | synonymous_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.98 |
embB | 4245626 | c.-888G>A | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |