Run ID: SRR25827445
Sample name:
Date: 21-03-2024 08:36:29
Number of reads: 7331874
Percentage reads mapped: 98.78
Strain: lineage3;lineage1.1.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Leu452Pro (0.49) |
Isoniazid | R | katG p.Ser315Thr (0.58) |
Ethambutol | R | embB p.Met306Leu (0.56) |
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.45 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.52 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.53 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.53 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.49 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.58 | isoniazid |
embB | 4247429 | p.Met306Leu | missense_variant | 0.56 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.54 |
gyrB | 6124 | c.885C>T | synonymous_variant | 0.51 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.53 |
gyrA | 9047 | c.1746C>T | synonymous_variant | 0.53 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.54 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9443 | c.2142G>A | synonymous_variant | 0.56 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576000 | p.Asp218Ala | missense_variant | 0.53 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.52 |
rpoB | 760490 | c.684C>T | synonymous_variant | 0.52 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.4 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.52 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.52 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.53 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 0.54 |
mmpR5 | 779261 | p.Thr91Ile | missense_variant | 0.51 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.48 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472485 | n.640G>A | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476436 | n.2779A>G | non_coding_transcript_exon_variant | 0.47 |
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 | 2167983 | p.Gly877Asp | missense_variant | 0.49 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.58 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.47 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.51 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.54 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.48 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.48 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.53 |
Rv2752c | 3065305 | p.Ala296Val | missense_variant | 0.52 |
Rv2752c | 3065748 | p.His148Gln | missense_variant | 0.55 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087583 | c.768_769dupGC | frameshift_variant | 0.5 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.53 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.5 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.55 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.53 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.53 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.56 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.42 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 0.49 |
embA | 4245835 | p.Leu868Arg | missense_variant | 0.18 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.52 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.5 |
aftB | 4269096 | c.-260C>G | upstream_gene_variant | 0.38 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.49 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.45 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.47 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.5 |
gid | 4407980 | p.Pro75Ser | missense_variant | 0.53 |