Run ID: ERR751349
Sample name:
Date: 19-10-2023 20:34:46
Number of reads: 4782857
Percentage reads mapped: 99.55
Strain: lineage5.1.1;lineage4.8
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 | 0.73 |
lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.33 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.68 |
lineage5.1 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.29 |
lineage5.1.1 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.3 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.44 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.32 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.31 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.25 |
gyrA | 9566 | c.2265C>T | synonymous_variant | 0.29 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.38 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.27 |
rpoC | 763280 | c.-90C>T | upstream_gene_variant | 0.26 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.21 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.24 |
Rv1258c | 1407273 | p.Asp23Val | missense_variant | 0.25 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.32 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101840 | c.1203G>A | synonymous_variant | 0.29 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.29 |
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 0.27 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.28 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.28 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.68 |
Rv1979c | 2222569 | p.Ala199Val | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.99 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 0.29 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.31 |
ald | 3087084 | c.266delA | frameshift_variant | 0.27 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 0.25 |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.31 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.32 |
alr | 3840932 | c.489C>T | synonymous_variant | 0.38 |
rpoA | 3878493 | c.15G>A | synonymous_variant | 0.3 |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.3 |
ddn | 3987180 | p.Asp113Asn | missense_variant | 0.33 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.76 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 0.39 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.25 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.24 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 0.26 |
embA | 4244635 | p.Val468Ala | missense_variant | 0.35 |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.34 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.28 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.28 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.3 |
aftB | 4269768 | c.-932C>A | upstream_gene_variant | 0.22 |
ethR | 4326928 | c.-621G>A | upstream_gene_variant | 0.32 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 0.35 |
whiB6 | 4338547 | c.-26A>G | upstream_gene_variant | 0.22 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.34 |