Run ID: ERR4821880
Sample name:
Date: 01-04-2023 17:30:23
Number of reads: 392756
Percentage reads mapped: 82.02
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 | 0.99 |
lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 0.95 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.75 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.92 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
folC | 2747471 | p.Ile43Thr | missense_variant | 1.0 | para-aminosalicylic_acid |
ethA | 4326419 | c.1054delG | frameshift_variant | 0.83 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5500 | c.261C>T | synonymous_variant | 0.2 |
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 | 7882 | p.Leu194Pro | missense_variant | 0.17 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.73 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.92 |
gyrA | 9171 | p.Val624Leu | missense_variant | 0.22 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490811 | p.Ala10Val | missense_variant | 0.89 |
fgd1 | 490819 | p.Glu13Lys | missense_variant | 0.25 |
fgd1 | 491426 | p.Ala215Val | missense_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576376 | c.1029G>A | synonymous_variant | 0.12 |
rpoB | 761722 | p.Glu639Gly | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 765988 | c.2619G>A | synonymous_variant | 0.83 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.75 |
mmpL5 | 776868 | p.Arg538Gln | missense_variant | 0.22 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781904 | p.Ser115Arg | missense_variant | 0.29 |
fbiC | 1305229 | p.Arg767Cys | missense_variant | 0.33 |
Rv1258c | 1406365 | p.Gly326* | stop_gained | 0.15 |
Rv1258c | 1406479 | p.Arg288Ser | missense_variant | 0.2 |
Rv1258c | 1406797 | p.Gly182Arg | missense_variant | 0.12 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1461049 | p.Asp2Gly | missense_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.86 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472620 | n.775A>G | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.92 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.92 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.93 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.86 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1474252 | n.595T>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.5 |
fabG1 | 1673343 | c.-96delC | upstream_gene_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918033 | p.Val32Leu | missense_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155917 | c.195C>A | synonymous_variant | 0.4 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.86 |
Rv1979c | 2221791 | c.1374G>T | synonymous_variant | 0.17 |
Rv1979c | 2221909 | p.Leu419Pro | missense_variant | 0.33 |
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 | 0.93 |
kasA | 2518183 | c.69G>A | synonymous_variant | 0.12 |
eis | 2714807 | c.525delT | frameshift_variant | 0.12 |
eis | 2714990 | p.Val115Ile | missense_variant | 0.12 |
eis | 2715005 | c.327delC | frameshift_variant | 0.14 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.86 |
ahpC | 2726468 | c.276G>A | synonymous_variant | 0.9 |
folC | 2746237 | c.1362G>C | synonymous_variant | 0.17 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3064715 | p.His493Asn | missense_variant | 0.29 |
Rv2752c | 3065780 | p.Val138Leu | missense_variant | 0.2 |
thyX | 3067491 | p.Ala152Val | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448631 | p.Gly43Asp | missense_variant | 0.18 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448882 | c.382dupA | frameshift_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 0.89 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.83 |
fprA | 3475313 | p.Pro436Gln | missense_variant | 0.4 |
Rv3236c | 3612223 | c.894C>G | synonymous_variant | 1.0 |
Rv3236c | 3612495 | c.622C>A | synonymous_variant | 0.4 |
Rv3236c | 3612581 | p.Leu179Pro | missense_variant | 1.0 |
Rv3236c | 3612942 | p.Ala59Thr | missense_variant | 0.29 |
fbiA | 3641341 | p.Ser267Pro | missense_variant | 0.14 |
fbiB | 3642512 | c.978G>A | synonymous_variant | 0.12 |
clpC1 | 4038566 | c.2139C>A | synonymous_variant | 0.4 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239761 | c.-102C>T | upstream_gene_variant | 0.25 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.75 |
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 | 4244873 | c.1641C>T | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248083 | p.Arg524Cys | missense_variant | 0.15 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4270027 | c.-194C>T | upstream_gene_variant | 0.12 |
ethA | 4327451 | p.Val8Asp | missense_variant | 0.29 |
ethA | 4328212 | c.-740delC | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.8 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |