Run ID: ERR4798523
Sample name:
Date: 01-04-2023 08:25:59
Number of reads: 1971070
Percentage reads mapped: 50.52
Strain: lineage1.2.2.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 1.0 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761140 | p.His445Arg | missense_variant | 1.0 | rifampicin |
fabG1 | 1673432 | c.-8T>C | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.99 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_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 | 765816 | p.Thr816Met | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777431 | c.1047_1049delCGC | disruptive_inframe_deletion | 1.0 |
mmpS5 | 779625 | c.-720G>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471862 | n.17T>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472582 | n.738_739delTA | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472697 | n.852T>G | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472836 | n.991G>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472842 | n.997G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475792 | n.2135G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475935 | n.2278T>A | non_coding_transcript_exon_variant | 0.5 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102240 | p.Arg268His | missense_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 |
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 | 0.98 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2747468 | p.Asp44Gly | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | 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 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
aftB | 4267960 | p.Val293Met | missense_variant | 0.97 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407799 | p.Val135Ala | missense_variant | 1.0 |
gid | 4407848 | p.Ala119Thr | missense_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |