Run ID: ERR2229235
Sample name:
Date: 31-03-2023 16:50:40
Number of reads: 455083
Percentage reads mapped: 99.15
Strain: lineage4.8
Drug-resistance: RR-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 | 761144 | p.Lys446Asn | missense_variant | 0.22 | rifampicin |
pncA | 2289099 | p.Lys48Thr | missense_variant | 0.29 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 8064 | p.Gly255Arg | missense_variant | 0.14 |
gyrA | 8952 | p.Gln551Lys | missense_variant | 0.14 |
fgd1 | 491021 | p.Arg80His | missense_variant | 0.12 |
rpoB | 761048 | c.1242C>A | synonymous_variant | 0.22 |
rpoB | 761915 | p.Asp703Glu | missense_variant | 0.29 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777119 | p.His454Gln | missense_variant | 0.2 |
mmpL5 | 777122 | c.1359C>T | synonymous_variant | 0.2 |
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.2 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473612 | n.-46A>G | upstream_gene_variant | 0.15 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
inhA | 1674732 | c.531C>T | synonymous_variant | 0.29 |
rpsA | 1833464 | c.-78A>G | upstream_gene_variant | 0.2 |
tlyA | 1917862 | c.-78G>T | upstream_gene_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102345 | p.Ala233Asp | missense_variant | 0.2 |
ndh | 2102625 | p.Ser140Thr | missense_variant | 0.2 |
ndh | 2102632 | c.411C>A | synonymous_variant | 0.2 |
katG | 2154170 | p.Glu648Lys | missense_variant | 0.15 |
katG | 2155286 | p.His276Asn | missense_variant | 0.22 |
PPE35 | 2167746 | p.Thr956Ile | missense_variant | 0.2 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.15 |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.15 |
PPE35 | 2168383 | p.Phe744Ile | missense_variant | 0.25 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2168807 | c.1806C>T | synonymous_variant | 0.14 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.11 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.12 |
PPE35 | 2169378 | p.Phe412Tyr | missense_variant | 0.14 |
PPE35 | 2169717 | p.Asn299Ile | missense_variant | 0.18 |
PPE35 | 2169732 | p.Asn294Ser | missense_variant | 0.18 |
PPE35 | 2169868 | p.Ser249Pro | missense_variant | 0.12 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.25 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.22 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.31 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.38 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289898 | c.-657C>A | upstream_gene_variant | 0.29 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.38 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.38 |
kasA | 2519225 | p.Leu371Met | missense_variant | 0.22 |
eis | 2714309 | p.Pro342Ser | missense_variant | 0.14 |
ribD | 2987435 | c.600delG | frameshift_variant | 0.2 |
thyX | 3067806 | p.Trp47Ser | missense_variant | 0.18 |
thyA | 3074136 | c.336C>A | synonymous_variant | 0.25 |
thyA | 3074173 | p.Ser100Leu | missense_variant | 0.22 |
ald | 3087237 | p.Leu140Ile | missense_variant | 0.2 |
fprA | 3474143 | p.Trp46Tyr | missense_variant | 0.15 |
fprA | 3474165 | c.159C>G | synonymous_variant | 0.2 |
alr | 3840517 | p.Pro302Thr | missense_variant | 0.18 |
alr | 3841019 | c.402G>A | synonymous_variant | 0.12 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.24 |
clpC1 | 4038651 | p.Gly685Val | missense_variant | 0.25 |
embC | 4240848 | p.Asp329Gly | missense_variant | 0.12 |
embC | 4241367 | p.Leu502His | missense_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4246260 | p.Asp1010Tyr | missense_variant | 0.29 |
embB | 4246527 | p.Ala5Glu | missense_variant | 0.4 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.25 |
embB | 4246591 | c.78G>A | synonymous_variant | 0.15 |
embB | 4249064 | p.Gly851Cys | missense_variant | 0.22 |
aftB | 4268217 | p.Trp207* | stop_gained | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 |