Run ID: ERR2514142
Sample name:
Date: 31-03-2023 20:08:39
Number of reads: 769327
Percentage reads mapped: 98.62
Strain: lineage1.2.2.2
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.98 |
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 |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
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 |
gyrA | 9681 | p.Ala794Thr | missense_variant | 0.13 |
gyrA | 9704 | c.2403T>A | synonymous_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576646 | c.1299C>T | synonymous_variant | 0.12 |
mshA | 576670 | p.Tyr441* | stop_gained | 0.12 |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.15 |
rpoB | 762236 | c.2430G>A | synonymous_variant | 0.14 |
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 | 766367 | p.Ala1000Thr | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778210 | p.Ala91Thr | missense_variant | 0.14 |
mmpS5 | 779625 | c.-720G>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800691 | c.-118A>G | upstream_gene_variant | 0.11 |
Rv1258c | 1406504 | c.837C>G | synonymous_variant | 0.11 |
Rv1258c | 1407198 | p.Ala48Asp | missense_variant | 0.17 |
Rv1258c | 1407200 | c.141G>T | synonymous_variant | 0.17 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472766 | n.921G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474469 | n.812T>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 |
inhA | 1674609 | c.408G>T | synonymous_variant | 0.18 |
rpsA | 1834669 | c.1128G>C | synonymous_variant | 0.12 |
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 |
PPE35 | 2169971 | c.642T>C | synonymous_variant | 0.13 |
PPE35 | 2170066 | p.Ala183Thr | missense_variant | 0.29 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289464 | c.-223A>T | upstream_gene_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2519107 | c.993T>C | synonymous_variant | 0.15 |
kasA | 2519108 | p.Asp332Gln | missense_variant | 0.15 |
kasA | 2519116 | c.1002C>G | synonymous_variant | 0.18 |
kasA | 2519122 | c.1008G>C | synonymous_variant | 0.14 |
kasA | 2519137 | c.1023T>G | synonymous_variant | 0.14 |
kasA | 2519158 | c.1044C>T | synonymous_variant | 0.14 |
kasA | 2519167 | c.1053T>G | synonymous_variant | 0.12 |
kasA | 2519170 | c.1056G>T | synonymous_variant | 0.12 |
kasA | 2519221 | c.1107G>C | synonymous_variant | 0.11 |
kasA | 2519230 | c.1116C>T | synonymous_variant | 0.11 |
eis | 2714307 | c.1025dupC | frameshift_variant | 0.11 |
eis | 2715468 | c.-136C>T | upstream_gene_variant | 0.17 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2747458 | c.141G>T | synonymous_variant | 0.12 |
ribD | 2986684 | c.-155T>C | upstream_gene_variant | 0.12 |
thyX | 3067589 | c.357G>A | synonymous_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339580 | p.Gly155Ser | missense_variant | 1.0 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449797 | p.Asp432Asn | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474143 | p.Trp46Tyr | missense_variant | 0.17 |
fprA | 3474165 | c.159C>G | synonymous_variant | 0.13 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiB | 3641517 | c.-18C>T | upstream_gene_variant | 0.11 |
fbiB | 3641994 | p.Arg154Cys | missense_variant | 0.11 |
fbiB | 3642636 | p.Ala368Ser | missense_variant | 0.15 |
rpoA | 3877776 | c.732T>C | synonymous_variant | 0.1 |
rpoA | 3877782 | c.726T>C | synonymous_variant | 0.11 |
rpoA | 3877785 | c.723C>G | synonymous_variant | 0.12 |
rpoA | 3877797 | c.711G>A | synonymous_variant | 0.11 |
rpoA | 3877818 | c.690A>G | synonymous_variant | 0.12 |
rpoA | 3877824 | c.684G>A | synonymous_variant | 0.12 |
rpoA | 3877839 | c.669G>C | synonymous_variant | 0.12 |
rpoA | 3878508 | c.-1C>T | upstream_gene_variant | 0.17 |
ddn | 3986853 | p.Ser4Thr | missense_variant | 0.11 |
clpC1 | 4038173 | p.Glu844Asp | missense_variant | 0.4 |
clpC1 | 4038755 | c.1950G>T | synonymous_variant | 0.11 |
clpC1 | 4038773 | c.1932T>C | synonymous_variant | 0.12 |
clpC1 | 4038782 | c.1923G>T | synonymous_variant | 0.12 |
clpC1 | 4038790 | c.1915C>T | synonymous_variant | 0.12 |
clpC1 | 4038812 | c.1893T>C | synonymous_variant | 0.11 |
clpC1 | 4038838 | c.1867C>T | synonymous_variant | 0.12 |
clpC1 | 4038949 | p.His586Tyr | missense_variant | 0.17 |
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 |
embC | 4241552 | p.Pro564Ser | missense_variant | 0.11 |
embC | 4241617 | c.1755G>A | synonymous_variant | 0.12 |
embA | 4242415 | c.-818G>A | upstream_gene_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244184 | p.Ser318Arg | missense_variant | 0.11 |
embA | 4244340 | p.Ser370Thr | missense_variant | 0.11 |
embA | 4245183 | p.Leu651Met | missense_variant | 0.11 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249323 | p.Ala937Glu | missense_variant | 0.2 |
aftB | 4267954 | p.Ala295Pro | missense_variant | 0.15 |
aftB | 4267960 | p.Val293Met | missense_variant | 1.0 |
aftB | 4268548 | p.Leu97Met | missense_variant | 0.13 |
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 |
ethR | 4327579 | p.Leu11Met | missense_variant | 0.18 |
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 | 4407848 | p.Ala119Thr | missense_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |