Run ID: SRR1165277
Sample name:
Date: 02-04-2023 23:57:21
Number of reads: 3986684
Percentage reads mapped: 95.65
Strain: lineage4.3.3
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 0.97 | isoniazid |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol |
ethA | 4327484 | c.-11A>G | upstream_gene_variant | 0.97 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576583 | c.1236A>C | synonymous_variant | 0.12 |
rpoC | 764510 | c.1141C>T | synonymous_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 766708 | c.3340_3342dupGGC | conservative_inframe_insertion | 0.35 |
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 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223051 | p.Glu38Asp | missense_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 0.99 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244329 | c.1098_1099dupGG | frameshift_variant | 0.13 |
embA | 4244909 | c.1686_1688dupGCT | disruptive_inframe_insertion | 0.1 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
gid | 4407912 | c.160_290del | frameshift_variant | 1.0 |