Run ID: ERR4818346
Sample name:
Date: 01-04-2023 15:30:30
Number of reads: 1095108
Percentage reads mapped: 99.1
Strain: lineage4.1.1.3.1
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 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.99 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
lineage4.1.1.3.1 | Euro-American (X-type) | X1;X3 | RD193 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 1.0 | rifampicin |
embB | 4247431 | p.Met306Ile | missense_variant | 0.93 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 765084 | p.Arg572His | missense_variant | 0.19 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 765920 | p.Ile851Val | missense_variant | 0.36 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775883 | p.Ile866Leu | missense_variant | 0.12 |
mmpL5 | 775918 | p.Val855Ile | missense_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303601 | p.Glu224Gly | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472123 | n.278A>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472150 | n.305T>G | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472151 | n.306C>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.25 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.17 |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.17 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.18 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.17 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.12 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.14 |
Rv2752c | 3067066 | c.-876delG | upstream_gene_variant | 0.11 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474143 | p.Trp46Tyr | missense_variant | 0.12 |
fprA | 3474165 | c.159C>G | synonymous_variant | 0.1 |
clpC1 | 4039829 | p.Leu292Phe | missense_variant | 0.1 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
aftB | 4269540 | c.-704C>T | upstream_gene_variant | 1.0 |
ethR | 4327309 | c.-240G>C | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |