Run ID: ERR1063888
Sample name:
Date: 31-03-2023 10:32:32
Number of reads: 2990054
Percentage reads mapped: 89.75
Strain: lineage1.1.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6124 | c.885C>T | synonymous_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 | 765171 | p.Pro601Leu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.98 |
mmpL5 | 776100 | p.Thr794Ile | missense_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 | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472803 | n.958T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472953 | n.1108G>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472970 | n.1125C>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472977 | n.1132G>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472982 | n.1137G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473001 | n.1156G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473002 | n.1157G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473008 | n.1163C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473009 | n.1164T>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473020 | n.1175T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476229 | n.2572C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476251 | n.2594T>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476256 | n.2599A>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476297 | n.2640C>A | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.21 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.98 |
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 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339741 | c.624G>A | synonymous_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 | 0.98 |
fprA | 3474700 | p.Gly232Ser | missense_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
clpC1 | 4040517 | p.Val63Ala | missense_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 | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249673 | p.Ser1054Pro | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4328209 | c.-736C>A | upstream_gene_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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4407935 | p.Leu90Val | missense_variant | 1.0 |
gid | 4407944 | p.Gln87Glu | missense_variant | 1.0 |
gid | 4408070 | p.Trp45Arg | missense_variant | 1.0 |