Run ID: SRR1174291
Sample name:
Date: 03-04-2023 03:33:56
Number of reads: 1009150
Percentage reads mapped: 57.81
Strain: lineage1.1.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.99 |
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 | 2155693 | p.Ser140Asn | missense_variant | 0.2 | isoniazid |
ethA | 4326236 | p.Gly413Asp | missense_variant | 1.0 | ethionamide |
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 |
mshA | 576443 | p.Gly366Ser | missense_variant | 0.12 |
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 | 1.0 |
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 | 1472153 | n.308G>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472252 | n.407G>C | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.51 |
rrs | 1472785 | n.940G>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472814 | n.969G>A | non_coding_transcript_exon_variant | 0.49 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473038 | n.1193A>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.1 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473070 | n.1225G>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473071 | n.1226C>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473162 | n.1317C>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.69 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.62 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155674 | c.438G>T | synonymous_variant | 0.22 |
katG | 2155691 | c.421T>C | synonymous_variant | 0.2 |
katG | 2155696 | p.Ala139Gly | missense_variant | 0.21 |
katG | 2155704 | c.408C>G | synonymous_variant | 0.24 |
katG | 2155716 | c.396T>C | synonymous_variant | 0.22 |
katG | 2155722 | c.390G>C | synonymous_variant | 0.25 |
katG | 2155728 | c.384G>T | synonymous_variant | 0.27 |
katG | 2155734 | p.Met126Asn | missense_variant | 0.27 |
katG | 2155741 | p.Gly124Thr | missense_variant | 0.25 |
katG | 2155743 | p.Gly123Ser | missense_variant | 0.25 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | 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 | 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 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448771 | p.Thr90Ala | missense_variant | 0.14 |
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 |
whiB7 | 3568507 | p.Gln58Arg | missense_variant | 0.96 |
fbiA | 3640958 | p.Gly139Asp | missense_variant | 1.0 |
alr | 3841174 | p.Gly83Arg | 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 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
whiB6 | 4338441 | p.Tyr27* | stop_gained | 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 |