Run ID: ERR163943
Sample name:
Date: 20-10-2023 22:12:49
Number of reads: 3393509
Percentage reads mapped: 95.79
Strain: lineage4.3.4.2.1;lineage1.1.2
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | ||
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 |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.88 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.78 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.1 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.06 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.81 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 0.08 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.79 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.8 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.12 |
gyrB | 6124 | c.885C>T | synonymous_variant | 0.11 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.79 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.12 |
mshA | 576000 | p.Asp218Ala | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.11 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.81 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304757 | c.1827A>G | synonymous_variant | 0.66 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288724 | p.Glu173Gly | missense_variant | 0.75 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.13 |
Rv2752c | 3065305 | p.Ala296Val | missense_variant | 0.12 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.78 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.11 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.78 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.16 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.69 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.73 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 0.13 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.21 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.17 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.1 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.13 |
ethA | 4326682 | p.Phe264Leu | missense_variant | 0.18 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.18 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.81 |