Run ID: SRR22528536
Sample name:
Date: 04-04-2023 04:18:16
Number of reads: 1496814
Percentage reads mapped: 99.69
Strain: lineage4.4.1.1;lineage4.1.2.1
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 | 0.53 |
lineage4.4 | Euro-American | S;T | None | 0.49 |
lineage4.1.2 | Euro-American | T;H | None | 0.52 |
lineage4.4.1 | Euro-American (S-type) | S;T | None | 0.47 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.5 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 0.44 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.4 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.46 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.49 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8116 | p.Thr272Ile | missense_variant | 0.32 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.63 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.58 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.78 |
rpoB | 761528 | p.Asp574Glu | missense_variant | 0.52 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.45 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474284 | n.627G>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474480 | n.823T>A | non_coding_transcript_exon_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102990 | p.Val18Ala | missense_variant | 0.63 |
PPE35 | 2169059 | c.1554G>T | synonymous_variant | 0.14 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.29 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.52 |
thyA | 3074495 | c.-24C>T | upstream_gene_variant | 0.45 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.52 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.54 |
rpoA | 3878622 | c.-115C>G | upstream_gene_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.42 |
embA | 4244970 | c.1738C>T | synonymous_variant | 0.45 |
embB | 4246582 | c.69T>G | synonymous_variant | 0.12 |
embB | 4248437 | p.Thr642Ala | missense_variant | 0.36 |
aftB | 4268234 | c.603G>A | synonymous_variant | 0.18 |
ethR | 4326703 | c.-846T>C | upstream_gene_variant | 0.41 |
whiB6 | 4338514 | p.Tyr3Cys | missense_variant | 0.52 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408157 | p.Leu16Val | missense_variant | 0.28 |