Run ID: ERR2706950
Sample name:
Date: 31-03-2023 23:10:43
Number of reads: 5703700
Percentage reads mapped: 91.06
Strain: lineage5.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.97 |
lineage5.2 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.93 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288703 | p.Val180Gly | missense_variant | 0.99 | pyrazinamide |
folC | 2747141 | p.Glu153Gly | missense_variant | 0.99 | para-aminosalicylic_acid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5124 | c.-116T>C | upstream_gene_variant | 1.0 |
gyrB | 6238 | c.999G>A | synonymous_variant | 0.14 |
gyrB | 6253 | c.1014G>C | synonymous_variant | 0.15 |
gyrB | 6265 | c.1026C>T | synonymous_variant | 0.15 |
gyrB | 6292 | c.1053G>C | synonymous_variant | 0.14 |
gyrA | 6319 | c.-983G>C | upstream_gene_variant | 0.14 |
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.98 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9566 | c.2265C>T | synonymous_variant | 0.99 |
fgd1 | 491259 | c.477T>C | synonymous_variant | 0.14 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.24 |
rpoB | 761054 | c.1248G>A | synonymous_variant | 0.13 |
rpoB | 761060 | c.1254C>G | synonymous_variant | 0.13 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.15 |
rpoB | 761180 | c.1374A>C | synonymous_variant | 0.15 |
rpoB | 761183 | c.1377T>G | synonymous_variant | 0.14 |
rpoB | 761189 | c.1383T>G | synonymous_variant | 0.15 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.15 |
rpoB | 761198 | c.1392G>T | synonymous_variant | 0.14 |
rpoB | 761222 | c.1416G>C | synonymous_variant | 0.13 |
rpoB | 762114 | p.Ile770Val | missense_variant | 0.15 |
rpoB | 762122 | c.2316C>T | synonymous_variant | 0.14 |
rpoB | 762149 | c.2343G>C | synonymous_variant | 0.14 |
rpoB | 762233 | c.2427G>T | synonymous_variant | 0.16 |
rpoB | 762254 | c.2448T>G | synonymous_variant | 0.15 |
rpoB | 762338 | c.2532T>C | synonymous_variant | 0.18 |
rpoB | 762347 | c.2541T>C | synonymous_variant | 0.15 |
rpoB | 762353 | c.2547C>T | synonymous_variant | 0.16 |
rpoB | 762362 | p.Glu852Asp | missense_variant | 0.14 |
rpoB | 762369 | c.2563T>C | synonymous_variant | 0.14 |
rpoC | 762380 | c.-990T>G | upstream_gene_variant | 0.13 |
rpoC | 762410 | c.-960T>A | upstream_gene_variant | 0.15 |
rpoC | 762416 | c.-954A>G | upstream_gene_variant | 0.15 |
rpoC | 762434 | c.-936T>C | upstream_gene_variant | 0.16 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.18 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763034 | c.-336C>G | upstream_gene_variant | 0.18 |
rpoC | 763040 | c.-330C>G | upstream_gene_variant | 0.18 |
rpoC | 763070 | c.-300T>C | upstream_gene_variant | 0.18 |
rpoC | 763085 | c.-285C>G | upstream_gene_variant | 0.16 |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.15 |
rpoC | 763573 | c.204G>C | synonymous_variant | 0.16 |
rpoC | 763603 | c.234C>T | synonymous_variant | 0.15 |
rpoC | 763621 | c.252C>T | synonymous_variant | 0.14 |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.14 |
rpoC | 763636 | c.267T>C | synonymous_variant | 0.16 |
rpoC | 763657 | c.288G>A | synonymous_variant | 0.15 |
rpoC | 763660 | c.291T>G | synonymous_variant | 0.14 |
rpoC | 763666 | c.297G>T | synonymous_variant | 0.14 |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.16 |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.13 |
rpoC | 763978 | c.609C>G | synonymous_variant | 0.17 |
rpoC | 763996 | c.627T>C | synonymous_variant | 0.13 |
rpoC | 764002 | c.633C>G | synonymous_variant | 0.14 |
rpoC | 764005 | c.636G>C | synonymous_variant | 0.14 |
rpoC | 764746 | c.1377G>T | synonymous_variant | 0.14 |
rpoC | 764803 | c.1434C>T | synonymous_variant | 0.13 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.88 |
rpoC | 765700 | c.2331T>C | synonymous_variant | 0.14 |
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 |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473111 | n.1266A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474552 | n.895C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474638 | n.981C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474711 | n.1054G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474715 | n.1058T>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474716 | n.1059A>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474717 | n.1060A>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474753 | n.1096A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475995 | n.2338G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476033 | n.2376T>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476034 | n.2377C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476045 | n.2388G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476046 | n.2389G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476108 | n.2451T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476221 | n.2564T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476256 | n.2599A>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476529 | n.2872A>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476583 | n.2926G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476628 | n.2971T>C | non_coding_transcript_exon_variant | 0.16 |
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.99 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.99 |
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 |
Rv3083 | 3449324 | p.Arg274Gln | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568480 | p.Gly67Val | missense_variant | 1.0 |
alr | 3840932 | c.489C>T | synonymous_variant | 1.0 |
rpoA | 3877764 | c.744C>G | synonymous_variant | 0.15 |
rpoA | 3877770 | c.738A>G | synonymous_variant | 0.14 |
rpoA | 3877776 | c.732T>C | synonymous_variant | 0.14 |
rpoA | 3877848 | c.660C>T | synonymous_variant | 0.14 |
rpoA | 3878061 | c.447G>C | synonymous_variant | 0.13 |
rpoA | 3878067 | c.441C>G | synonymous_variant | 0.13 |
rpoA | 3878103 | c.405A>G | synonymous_variant | 0.14 |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.15 |
rpoA | 3878118 | c.390T>C | synonymous_variant | 0.16 |
rpoA | 3878130 | c.378C>G | synonymous_variant | 0.15 |
rpoA | 3878143 | p.Gly122Asp | missense_variant | 0.15 |
rpoA | 3878163 | c.345C>T | synonymous_variant | 0.17 |
rpoA | 3878184 | c.324C>A | synonymous_variant | 0.2 |
rpoA | 3878193 | c.315T>C | synonymous_variant | 0.19 |
rpoA | 3878217 | c.291A>G | synonymous_variant | 0.17 |
rpoA | 3878229 | c.279C>G | synonymous_variant | 0.2 |
rpoA | 3878232 | c.276G>C | synonymous_variant | 0.19 |
rpoA | 3878271 | c.237T>C | synonymous_variant | 0.15 |
rpoA | 3878283 | p.Glu75Asp | missense_variant | 0.18 |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.18 |
rpoA | 3878298 | c.210A>G | synonymous_variant | 0.2 |
rpoA | 3878304 | c.204G>T | synonymous_variant | 0.2 |
rpoA | 3878313 | c.195G>C | synonymous_variant | 0.18 |
rpoA | 3878322 | c.186A>G | synonymous_variant | 0.19 |
rpoA | 3878331 | c.177A>G | synonymous_variant | 0.18 |
rpoA | 3878337 | c.171T>C | synonymous_variant | 0.17 |
rpoA | 3878346 | c.162T>C | synonymous_variant | 0.18 |
rpoA | 3878358 | c.150C>G | synonymous_variant | 0.19 |
rpoA | 3878361 | c.147G>T | synonymous_variant | 0.2 |
rpoA | 3878364 | c.144A>C | synonymous_variant | 0.19 |
rpoA | 3878385 | c.123C>G | synonymous_variant | 0.18 |
rpoA | 3878391 | c.117T>G | synonymous_variant | 0.18 |
rpoA | 3878400 | c.108T>C | synonymous_variant | 0.18 |
rpoA | 3878409 | c.99C>G | synonymous_variant | 0.19 |
rpoA | 3878436 | c.72A>G | synonymous_variant | 0.14 |
ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 |
ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 |
clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244220 | c.988C>T | synonymous_variant | 0.99 |
embA | 4244635 | p.Val468Ala | missense_variant | 1.0 |
embA | 4245147 | p.Pro639Ser | missense_variant | 0.96 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.99 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326279 | p.Ser399Pro | missense_variant | 0.99 |
ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |