Run ID: ERR164021
Sample name:
Date: 31-03-2023 14:53:23
Number of reads: 8921572
Percentage reads mapped: 94.99
Strain: lineage4.3.4.2.1;lineage1.2.2.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.69 |
lineage1 | Indo-Oceanic | EAI | RD239 | 0.32 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.68 |
lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.29 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.69 |
lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.31 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.7 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.7 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Asn | missense_variant | 0.27 | rifampicin |
rrs | 1472359 | n.514A>T | non_coding_transcript_exon_variant | 0.23 | streptomycin |
inhA | 1674481 | p.Ser94Ala | missense_variant | 0.28 | isoniazid, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.27 |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.24 |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.77 |
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.27 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.27 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.27 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.3 |
rpoC | 763552 | c.183C>T | synonymous_variant | 0.28 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.27 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.28 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.73 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.25 |
mmpL5 | 777017 | c.1464C>T | synonymous_variant | 0.65 |
mmpS5 | 779625 | c.-720G>A | upstream_gene_variant | 0.27 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473070 | n.1225G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473089 | n.1244A>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473094 | n.1249T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473097 | n.1252G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473099 | n.1254T>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.11 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102240 | p.Arg268His | missense_variant | 0.29 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.26 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.29 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.32 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.25 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.28 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.29 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.74 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.24 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.35 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.37 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.66 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.67 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.76 |
clpC1 | 4038328 | p.Glu793Gln | missense_variant | 0.26 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.27 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.3 |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.3 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.3 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.27 |
embA | 4242559 | c.-674G>A | upstream_gene_variant | 0.4 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245670 | p.Ala813Gly | missense_variant | 0.28 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.34 |
embB | 4246979 | p.Gly156Cys | missense_variant | 0.35 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.32 |
aftB | 4267960 | p.Val293Met | missense_variant | 0.2 |
ubiA | 4269162 | p.Leu224Phe | missense_variant | 0.29 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.36 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.3 |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.27 |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.33 |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.32 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.27 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.25 |
gid | 4407848 | p.Ala119Thr | missense_variant | 0.29 |
gid | 4407873 | c.330G>T | synonymous_variant | 0.26 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.72 |