Run ID: ERR4553573
Sample name:
Date: 01-04-2023 06:13:48
Number of reads: 885004
Percentage reads mapped: 99.57
Strain: lineage1.1.3.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.12 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 1.0 |
lineage1.1.3.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289016 | p.Thr76Pro | missense_variant | 0.24 | pyrazinamide |
embB | 4248025 | p.Glu504Asp | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5121 | c.-119A>T | upstream_gene_variant | 0.67 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6767 | p.Gly510Ser | missense_variant | 0.11 |
gyrA | 7051 | c.-251A>G | upstream_gene_variant | 1.0 |
gyrB | 7124 | p.Ser629Ala | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.89 |
rpoC | 764689 | c.1320G>A | synonymous_variant | 1.0 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416937 | p.His137Gln | missense_variant | 0.14 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471946 | n.101C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474234 | n.577G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474296 | n.639T>A | non_coding_transcript_exon_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167769 | p.Ser948Arg | missense_variant | 0.2 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2168709 | p.Asn635Ile | missense_variant | 0.11 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2747182 | c.417G>A | synonymous_variant | 1.0 |
ribD | 2987570 | c.732C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339521 | p.His135Arg | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
alr | 3841253 | c.168C>T | synonymous_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.33 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
whiB6 | 4338429 | c.-218_92del | frameshift_variant&start_lost | 1.0 |