Run ID: SRR3105761
Sample name:
Date: 04-04-2023 05:08:13
Number of reads: 578310
Percentage reads mapped: 98.5
Strain: lineage4.8
Drug-resistance: Pre-XDR-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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2289072 | p.His57Arg | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326059 | c.1411_1414dupGGCA | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
fgd1 | 490696 | c.-87T>G | upstream_gene_variant | 0.33 |
rpoC | 767314 | p.Tyr1315* | stop_gained | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781407 | c.-153C>T | upstream_gene_variant | 0.4 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rpsA | 1833852 | p.Lys104Thr | missense_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.67 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv1979c | 2223346 | c.-182C>A | upstream_gene_variant | 0.2 |
rpoA | 3877850 | p.Gly220Ser | missense_variant | 0.91 |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.83 |
embC | 4240616 | p.Asp252His | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |