Run ID: SRR6896250
Sample name:
Date: 04-04-2023 18:00:11
Number of reads: 971938
Percentage reads mapped: 91.26
Strain: lineage4.8.1
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 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
lineage4.8.1 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761004 | p.Thr400Ala | missense_variant | 1.0 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.11 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288790 | p.Leu151Ser | missense_variant | 0.97 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethA | 4327268 | p.Trp69* | stop_gained | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
mshA | 576007 | c.663_667delCAGGC | frameshift_variant | 0.96 |
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 | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
fbiD | 3339040 | c.-78T>C | upstream_gene_variant | 1.0 |
fbiB | 3642874 | p.Leu447Arg | 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 |