Run ID: SRR1173724
Sample name:
Date: 03-04-2023 03:30:44
Number of reads: 3925581
Percentage reads mapped: 99.41
Strain: lineage4.8;lineage4.1.1.3
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 |
lineage4.1 | Euro-American | T;X;H | None | 0.41 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.61 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.42 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 0.38 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.68 | streptomycin |
rrs | 1472723 | n.878G>A | non_coding_transcript_exon_variant | 0.36 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.34 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288782 | p.Arg154Gly | missense_variant | 0.42 | pyrazinamide |
pncA | 2289067 | p.Ser59Pro | missense_variant | 0.47 | pyrazinamide |
ald | 3087278 | c.464delG | frameshift_variant | 0.44 | cycloserine |
embA | 4243217 | c.-16C>G | upstream_gene_variant | 0.42 | ethambutol |
embB | 4247429 | p.Met306Val | missense_variant | 0.46 | ethambutol |
ethA | 4326279 | c.1192_1194dupGTG | conservative_inframe_insertion | 0.34 | ethionamide |
ethA | 4326604 | c.869dupA | frameshift_variant | 0.39 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6815 | p.Lys526Gln | missense_variant | 0.66 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.44 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.37 |
rpoB | 762285 | p.Arg827Cys | missense_variant | 0.48 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.47 |
rpoC | 766485 | p.Val1039Ala | missense_variant | 0.68 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781435 | c.-125G>C | upstream_gene_variant | 0.47 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.63 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154769 | p.Asp448Ala | missense_variant | 0.71 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.52 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.47 |
alr | 3840764 | c.657G>C | synonymous_variant | 0.43 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.34 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.43 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407798 | c.405G>T | synonymous_variant | 0.35 |