Run ID: ERR038747
Sample name:
Date: 31-03-2023 08:41:40
Number of reads: 15070519
Percentage reads mapped: 99.6
Strain: lineage4.8
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 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761076 | p.Phe424Val | missense_variant | 1.0 | rifampicin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin |
katG | 2154255 | c.1856dupT | frameshift_variant | 1.0 | isoniazid |
pncA | 2289043 | p.Ser67Pro | missense_variant | 0.95 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326696 | c.773_777dupGGCGC | frameshift_variant | 0.97 | ethionamide |
gid | 4408115 | c.87delC | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoB | 762276 | p.Arg824Ser | missense_variant | 1.0 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.25 |
rpoC | 767305 | p.Tyr1312* | stop_gained | 0.24 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777399 | p.Thr361Arg | missense_variant | 0.19 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
atpE | 1461019 | c.-26C>A | upstream_gene_variant | 0.24 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474380 | n.723G>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.21 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.42 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714366 | p.Val323Leu | missense_variant | 0.23 |
eis | 2715586 | c.-254G>C | upstream_gene_variant | 0.41 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.18 |
Rv2752c | 3064552 | p.Arg547Pro | missense_variant | 0.25 |
Rv2752c | 3064741 | p.Gly484Ala | missense_variant | 0.26 |
Rv2752c | 3066004 | c.187delG | frameshift_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.27 |
ald | 3086767 | c.-53A>C | upstream_gene_variant | 0.99 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
fbiB | 3642734 | c.1200G>C | synonymous_variant | 0.21 |
fbiB | 3642772 | p.Asp413Ala | missense_variant | 0.21 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.21 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.3 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.19 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.22 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.19 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.99 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.44 |
embC | 4242827 | p.Leu989Val | missense_variant | 0.2 |
aftB | 4267715 | c.1122G>A | synonymous_variant | 1.0 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.23 |
ethA | 4327672 | c.-199G>A | upstream_gene_variant | 0.29 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |