Run ID: ERR2517058
Sample name:
Date: 31-03-2023 21:54:49
Number of reads: 1178940
Percentage reads mapped: 99.73
Strain: lineage3
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5704 | c.465C>A | synonymous_variant | 0.25 |
gyrB | 5813 | p.Arg192Ser | missense_variant | 0.31 |
gyrB | 6653 | p.Asp472His | missense_variant | 0.14 |
gyrA | 7275 | c.-27C>A | upstream_gene_variant | 0.14 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491576 | p.Pro265Gln | missense_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 761193 | p.Gly463Trp | missense_variant | 0.2 |
rpoB | 761457 | p.Pro551Thr | missense_variant | 0.14 |
rpoB | 762432 | p.Gly876Trp | missense_variant | 0.29 |
rpoB | 762464 | p.Lys886Asn | missense_variant | 0.25 |
rpoC | 762617 | c.-753C>A | upstream_gene_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763669 | c.300C>A | synonymous_variant | 0.18 |
rpoC | 764260 | p.Lys297Asn | missense_variant | 0.15 |
rpoC | 764292 | p.Ser308* | stop_gained | 0.25 |
rpoC | 766141 | c.2772C>A | synonymous_variant | 0.16 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776399 | p.Glu694Asp | missense_variant | 0.11 |
mmpR5 | 779254 | p.Arg89Trp | missense_variant | 0.21 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416944 | p.Ser135Ile | missense_variant | 0.15 |
embR | 1417038 | p.Ser104Arg | missense_variant | 1.0 |
atpE | 1461212 | c.168C>A | synonymous_variant | 0.22 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471843 | n.-3G>T | upstream_gene_variant | 0.18 |
rrs | 1473152 | n.1307T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1473837 | n.180G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474792 | n.1135C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474959 | n.1302C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475360 | n.1703G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475639 | n.1982C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476720 | n.3063G>T | non_coding_transcript_exon_variant | 0.25 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.23 |
fabG1 | 1673513 | p.Arg25Leu | missense_variant | 0.2 |
rpsA | 1834204 | p.Asn221Lys | missense_variant | 0.2 |
rpsA | 1834227 | p.Gly229Asp | missense_variant | 0.18 |
rpsA | 1834241 | p.Leu234Met | missense_variant | 0.18 |
rpsA | 1834284 | p.Pro248Gln | missense_variant | 0.17 |
rpsA | 1834756 | p.Glu405Asp | missense_variant | 0.23 |
rpsA | 1834799 | p.Glu420* | stop_gained | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154263 | p.Leu617Ile | missense_variant | 0.13 |
katG | 2154299 | p.Pro605Thr | missense_variant | 0.17 |
katG | 2154414 | c.1698C>A | synonymous_variant | 0.25 |
katG | 2154545 | p.Glu523* | stop_gained | 0.25 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155938 | p.Met58Ile | missense_variant | 0.18 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168238 | p.Pro792Gln | missense_variant | 0.2 |
PPE35 | 2168904 | p.Ile570Thr | missense_variant | 0.2 |
PPE35 | 2169269 | c.1344A>G | synonymous_variant | 0.12 |
PPE35 | 2169272 | c.1341C>G | synonymous_variant | 0.11 |
PPE35 | 2169278 | c.1335T>C | synonymous_variant | 0.12 |
PPE35 | 2169281 | c.1332T>G | synonymous_variant | 0.12 |
PPE35 | 2169287 | c.1326T>C | synonymous_variant | 0.12 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.13 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
pncA | 2290033 | c.-792C>A | upstream_gene_variant | 0.4 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726285 | c.93C>A | synonymous_variant | 0.21 |
Rv2752c | 3064917 | c.1275C>T | synonymous_variant | 1.0 |
Rv2752c | 3065439 | c.753C>A | synonymous_variant | 0.15 |
Rv2752c | 3066138 | c.54C>A | synonymous_variant | 0.16 |
thyX | 3067971 | c.-26T>A | upstream_gene_variant | 0.12 |
thyA | 3074294 | p.Leu60Met | missense_variant | 0.12 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449105 | p.Pro201His | missense_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475021 | p.Gly339Trp | missense_variant | 0.15 |
fprA | 3475296 | p.Glu430Asp | missense_variant | 0.13 |
fprA | 3475331 | p.Val442Ala | missense_variant | 0.13 |
fprA | 3475371 | c.1365C>A | synonymous_variant | 0.25 |
Rv3236c | 3613280 | c.-164G>T | upstream_gene_variant | 0.2 |
alr | 3840625 | p.Leu266Ile | missense_variant | 0.18 |
rpoA | 3877502 | p.Tyr336His | missense_variant | 0.14 |
rpoA | 3877737 | c.771G>T | synonymous_variant | 0.15 |
rpoA | 3877963 | p.Arg182Leu | missense_variant | 0.18 |
rpoA | 3878207 | p.Gly101Cys | missense_variant | 0.17 |
embC | 4241654 | p.Gly598Trp | missense_variant | 0.18 |
embC | 4241663 | p.Gly601Trp | missense_variant | 0.18 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
aftB | 4267105 | p.Val578Leu | missense_variant | 0.13 |
aftB | 4267252 | p.Asp529His | missense_variant | 0.11 |
aftB | 4267981 | c.856C>A | synonymous_variant | 0.33 |
aftB | 4268014 | p.Pro275Thr | missense_variant | 0.22 |
aftB | 4268080 | p.Gly253Cys | missense_variant | 0.18 |
ubiA | 4269056 | p.Leu260Met | missense_variant | 0.19 |
ubiA | 4269714 | p.Leu40Phe | missense_variant | 0.22 |
ethR | 4327573 | p.Ala9Ser | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407603 | c.600G>T | synonymous_variant | 0.24 |