Run ID: ERR038739
Sample name:
Date: 31-03-2023 08:41:40
Number of reads: 25731319
Percentage reads mapped: 99.59
Strain: lineage4.6.1.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.6 | Euro-American | T;LAM | None | 1.0 |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 1.0 |
lineage4.6.1.2 | Euro-American | T2 | RD724 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289207 | p.Asp12Ala | missense_variant | 1.0 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol |
ethA | 4327147 | p.Trp109* | stop_gained | 0.99 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.31 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416410 | p.Leu313Arg | missense_variant | 1.0 |
atpE | 1461019 | c.-26C>A | upstream_gene_variant | 0.26 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.21 |
inhA | 1674465 | c.264C>T | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.18 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.37 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714366 | p.Val323Leu | missense_variant | 0.21 |
eis | 2715586 | c.-254G>C | upstream_gene_variant | 0.45 |
ahpC | 2726287 | p.Gly32Asp | missense_variant | 1.0 |
pepQ | 2859381 | c.1038C>G | synonymous_variant | 0.23 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.22 |
Rv2752c | 3064741 | p.Gly484Ala | missense_variant | 0.28 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.28 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3613029 | c.88T>C | synonymous_variant | 1.0 |
fbiB | 3641955 | p.Gly141Arg | missense_variant | 0.23 |
fbiB | 3642734 | c.1200G>C | synonymous_variant | 0.18 |
fbiB | 3642772 | p.Asp413Ala | missense_variant | 0.17 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.22 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.34 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.17 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.21 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.26 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.43 |
embA | 4243709 | c.477C>T | synonymous_variant | 1.0 |
embA | 4245055 | p.Thr608Asn | missense_variant | 1.0 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.25 |
ethA | 4327672 | c.-199G>A | upstream_gene_variant | 0.26 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 |
gid | 4408115 | p.Gly30Arg | missense_variant | 1.0 |