Run ID: ERR6336764
Sample name:
Date: 02-04-2023 02:02:23
Number of reads: 738157
Percentage reads mapped: 99.05
Strain: lineage1.2.1.2.1
Drug-resistance: Sensitive
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.1 | Indo-Oceanic | EAI2 | RD239 | 1.0 |
lineage1.2.1.2 | Indo-Oceanic | NA | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5534 | p.Val99Met | missense_variant | 0.67 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 6631 | c.-671C>T | upstream_gene_variant | 0.15 |
gyrA | 7346 | c.45C>T | synonymous_variant | 0.18 |
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 | 9079 | p.Gly593Glu | missense_variant | 0.2 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9260 | c.1959G>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491041 | p.Ala87Thr | missense_variant | 0.2 |
fgd1 | 491229 | c.447C>T | synonymous_variant | 0.13 |
fgd1 | 491451 | p.Asp223Glu | missense_variant | 0.22 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 576136 | c.789T>C | synonymous_variant | 0.22 |
ccsA | 620063 | p.Ser58Asn | missense_variant | 0.17 |
rpoB | 759925 | p.Glu40Gly | missense_variant | 0.17 |
rpoB | 759934 | p.Glu43Gly | missense_variant | 0.29 |
rpoB | 760029 | p.Asn75Asp | missense_variant | 0.15 |
rpoB | 760867 | p.Gly354Asp | missense_variant | 0.18 |
rpoB | 761152 | p.Leu449Gln | missense_variant | 0.33 |
rpoB | 761558 | c.1752C>T | synonymous_variant | 0.17 |
rpoB | 761742 | p.Glu646Lys | missense_variant | 0.17 |
rpoB | 762203 | c.2397G>A | synonymous_variant | 0.22 |
rpoB | 762864 | p.Gly1020Ser | missense_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 |
rpoC | 763773 | p.Val135Glu | missense_variant | 0.15 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764734 | p.Phe455Leu | missense_variant | 0.13 |
rpoC | 764964 | p.Phe532Ser | missense_variant | 0.11 |
rpoC | 765323 | p.Gly652Ser | missense_variant | 0.2 |
rpoC | 765685 | c.2316G>A | synonymous_variant | 0.17 |
rpoC | 766289 | p.Val974Met | missense_variant | 0.29 |
rpoC | 766736 | p.Arg1123Trp | missense_variant | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777773 | p.Val236Gly | missense_variant | 0.15 |
mmpS5 | 778614 | p.Ser98Thr | missense_variant | 0.15 |
mmpL5 | 778894 | c.-414T>C | upstream_gene_variant | 0.11 |
mmpL5 | 779166 | c.-686C>T | upstream_gene_variant | 0.2 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781702 | p.Ala48Gly | missense_variant | 0.15 |
rplC | 801161 | p.Ser118Phe | missense_variant | 0.12 |
rplC | 801275 | p.Thr156Met | missense_variant | 0.4 |
fbiC | 1303326 | c.396C>T | synonymous_variant | 0.14 |
fbiC | 1303815 | c.885C>T | synonymous_variant | 0.12 |
fbiC | 1304827 | p.Phe633Leu | missense_variant | 0.29 |
fbiC | 1305147 | c.2217C>T | synonymous_variant | 0.12 |
Rv1258c | 1406169 | p.Gly391Val | missense_variant | 0.29 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
Rv1258c | 1406502 | p.Val280Ala | missense_variant | 0.12 |
Rv1258c | 1406529 | p.Gly271Ala | missense_variant | 0.18 |
Rv1258c | 1407157 | p.Ala62Thr | missense_variant | 0.2 |
embR | 1416445 | c.903C>T | synonymous_variant | 0.4 |
embR | 1416962 | p.Gly129Asp | missense_variant | 0.5 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
embR | 1417077 | p.Arg91Trp | missense_variant | 0.25 |
embR | 1417087 | c.261G>T | synonymous_variant | 0.17 |
embR | 1417094 | p.Gly85Ala | missense_variant | 0.2 |
embR | 1417489 | c.-142G>C | upstream_gene_variant | 0.17 |
embR | 1417500 | c.-153C>T | upstream_gene_variant | 0.13 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1473086 | n.1241C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473137 | n.1292G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474515 | n.858G>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475004 | n.1347C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476562 | n.2908dupG | non_coding_transcript_exon_variant | 0.13 |
fabG1 | 1673317 | c.-123T>C | upstream_gene_variant | 0.11 |
fabG1 | 1673549 | p.Ala37Val | missense_variant | 0.4 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 |
inhA | 1674187 | c.-15A>G | upstream_gene_variant | 0.1 |
inhA | 1674935 | p.Leu245Arg | missense_variant | 0.2 |
rpsA | 1834929 | p.Ser463Leu | missense_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918535 | p.His199Arg | missense_variant | 0.11 |
ndh | 2101974 | p.Ala357Thr | missense_variant | 0.12 |
ndh | 2101985 | p.Gly353Asp | missense_variant | 0.13 |
ndh | 2102258 | p.Ser262Phe | missense_variant | 0.25 |
ndh | 2102754 | p.Gln97Glu | missense_variant | 0.25 |
katG | 2154602 | p.Gly504Arg | missense_variant | 0.2 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155394 | p.Asp240Asn | missense_variant | 0.22 |
katG | 2156300 | c.-189G>A | upstream_gene_variant | 0.15 |
katG | 2156367 | c.-256G>A | upstream_gene_variant | 0.25 |
PPE35 | 2167660 | p.Thr985Ala | missense_variant | 0.13 |
PPE35 | 2167772 | c.2841C>G | synonymous_variant | 0.13 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169123 | p.Thr497Ile | missense_variant | 0.12 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222783 | p.Ala128Thr | missense_variant | 0.2 |
Rv1979c | 2222870 | p.Ala99Thr | missense_variant | 0.13 |
Rv1979c | 2223269 | c.-105G>A | upstream_gene_variant | 0.29 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289323 | c.-82G>A | upstream_gene_variant | 0.12 |
pncA | 2289534 | c.-293G>C | upstream_gene_variant | 0.14 |
pncA | 2289539 | c.-298C>T | upstream_gene_variant | 0.14 |
kasA | 2517963 | c.-152G>A | upstream_gene_variant | 0.12 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
kasA | 2519215 | c.1101C>T | synonymous_variant | 0.5 |
kasA | 2519279 | c.1169_1170delGC | frameshift_variant | 0.25 |
eis | 2715150 | p.Met61Ile | missense_variant | 0.17 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726678 | c.486G>A | synonymous_variant | 0.33 |
ahpC | 2726746 | p.Leu185Arg | missense_variant | 0.25 |
folC | 2747044 | c.555C>T | synonymous_variant | 0.13 |
ribD | 2987032 | p.Pro65Leu | missense_variant | 0.14 |
Rv2752c | 3064822 | p.Val457Ala | missense_variant | 0.22 |
Rv2752c | 3064825 | p.Asp456Val | missense_variant | 0.22 |
Rv2752c | 3064828 | p.Gly455Asp | missense_variant | 0.25 |
thyX | 3067594 | p.Val118Leu | missense_variant | 0.12 |
thyA | 3073903 | p.Ala190Val | missense_variant | 0.2 |
thyA | 3074046 | c.426G>A | synonymous_variant | 0.17 |
thyA | 3074065 | p.Gly136Asp | missense_variant | 0.14 |
thyA | 3074441 | p.Val11Met | missense_variant | 0.14 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086925 | p.Gln36* | stop_gained | 0.18 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
Rv3083 | 3448669 | p.Asp56Asn | missense_variant | 0.12 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3448944 | c.441G>C | synonymous_variant | 0.14 |
Rv3083 | 3449140 | p.Ser213Ala | missense_variant | 0.22 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474076 | p.Lys24Glu | missense_variant | 0.15 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
Rv3236c | 3612548 | p.Ala190Val | missense_variant | 0.12 |
Rv3236c | 3612701 | c.415delG | frameshift_variant | 0.25 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiA | 3640687 | p.Asp49Asn | missense_variant | 0.22 |
fbiB | 3641253 | c.-282C>T | upstream_gene_variant | 0.18 |
fbiB | 3641849 | c.316delG | frameshift_variant | 0.12 |
fbiB | 3642653 | c.1119C>T | synonymous_variant | 0.14 |
fbiB | 3642671 | c.1137G>A | synonymous_variant | 0.17 |
alr | 3841471 | c.-51A>G | upstream_gene_variant | 0.17 |
rpoA | 3877586 | c.921delA | frameshift_variant | 0.22 |
rpoA | 3877646 | p.Asn288Tyr | missense_variant | 0.18 |
rpoA | 3877696 | p.Thr271Ser | missense_variant | 0.12 |
rpoA | 3877897 | p.Pro204Leu | missense_variant | 0.13 |
rpoA | 3878484 | c.24C>T | synonymous_variant | 0.13 |
rpoA | 3878668 | c.-161C>T | upstream_gene_variant | 0.4 |
clpC1 | 4039254 | p.Ile484Thr | missense_variant | 0.22 |
clpC1 | 4039828 | p.Val293Ile | missense_variant | 0.12 |
clpC1 | 4040081 | c.624C>T | synonymous_variant | 0.2 |
clpC1 | 4040146 | c.559C>T | synonymous_variant | 0.2 |
clpC1 | 4040170 | p.Thr179Ala | missense_variant | 0.2 |
clpC1 | 4040254 | p.Ala151Ser | missense_variant | 0.2 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4044110 | p.Tyr58Asp | missense_variant | 0.14 |
embC | 4239989 | c.127C>T | synonymous_variant | 0.25 |
embC | 4240172 | p.Val104Met | missense_variant | 0.14 |
embC | 4240411 | c.549G>C | synonymous_variant | 0.67 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241287 | c.1425G>A | synonymous_variant | 0.2 |
embC | 4241387 | p.Ser509Gly | missense_variant | 0.11 |
embC | 4241474 | c.1612C>T | synonymous_variant | 0.25 |
embA | 4242268 | c.-965T>C | upstream_gene_variant | 0.18 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4244883 | c.1652dupG | frameshift_variant | 0.2 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4247334 | p.Arg274His | missense_variant | 0.22 |
embB | 4247354 | p.Ala281Thr | missense_variant | 0.22 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247592 | p.Val360Ala | missense_variant | 0.11 |
embB | 4247593 | c.1081delT | frameshift_variant | 0.11 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4248637 | c.2124G>A | synonymous_variant | 0.4 |
embB | 4248810 | p.Pro766Leu | missense_variant | 0.29 |
embB | 4249487 | p.Leu992Val | missense_variant | 0.14 |
embB | 4249719 | p.Thr1069Ile | missense_variant | 0.13 |
aftB | 4267032 | p.Ile602Thr | missense_variant | 0.13 |
aftB | 4268760 | p.Trp26* | stop_gained | 0.2 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269393 | c.-557G>A | upstream_gene_variant | 0.13 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
ubiA | 4270011 | c.-178A>G | upstream_gene_variant | 0.14 |
ubiA | 4270016 | c.-183G>A | upstream_gene_variant | 0.22 |
ubiA | 4270021 | c.-188T>C | upstream_gene_variant | 0.2 |
ethA | 4327014 | p.Ser154Ala | missense_variant | 0.11 |
ethA | 4327479 | c.-6G>A | upstream_gene_variant | 0.18 |
whiB6 | 4338361 | p.Arg54Gln | 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 | 4407791 | p.Ala138Thr | missense_variant | 0.22 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4407933 | c.270C>T | synonymous_variant | 0.22 |
gid | 4408412 | c.-210G>A | upstream_gene_variant | 0.33 |