Run ID: ERR6336756
Sample name:
Date: 02-04-2023 02:02:24
Number of reads: 2195848
Percentage reads mapped: 98.93
Strain:
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 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7617 | p.Arg106Cys | missense_variant | 0.13 |
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
gyrA | 9109 | p.Gln603Arg | missense_variant | 0.11 |
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 |
gyrA | 9671 | p.Gln790His | missense_variant | 0.12 |
fgd1 | 491337 | c.555C>T | synonymous_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575169 | c.-179A>G | upstream_gene_variant | 0.12 |
mshA | 575172 | c.-176C>G | upstream_gene_variant | 0.12 |
mshA | 575310 | c.-38G>A | upstream_gene_variant | 0.22 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 576283 | c.936G>C | synonymous_variant | 0.22 |
mshA | 576401 | p.Ser352Pro | missense_variant | 0.18 |
mshA | 576665 | p.Ser440Gly | missense_variant | 0.22 |
mshA | 576729 | p.Ser461Leu | missense_variant | 0.25 |
ccsA | 620056 | p.Thr56Pro | missense_variant | 0.4 |
rpoB | 761373 | p.Val523Met | missense_variant | 0.14 |
rpoB | 761688 | p.Ala628Thr | missense_variant | 0.33 |
rpoB | 761704 | p.Gly633Asp | missense_variant | 0.17 |
rpoB | 761846 | c.2040G>A | synonymous_variant | 0.17 |
rpoB | 762294 | p.Ser830Pro | missense_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 764669 | p.Pro434Ser | missense_variant | 0.12 |
mmpL5 | 775626 | p.Trp952Ser | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775640 | c.2841C>A | synonymous_variant | 0.15 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776303 | c.2177delC | frameshift_variant | 0.22 |
mmpL5 | 777370 | p.Lys371Gln | missense_variant | 0.29 |
mmpL5 | 777886 | p.Ala199Thr | missense_variant | 0.12 |
mmpR5 | 778055 | c.-935G>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304044 | p.Pro372Ser | missense_variant | 0.33 |
fbiC | 1304377 | c.1447C>T | synonymous_variant | 0.2 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
embR | 1416441 | c.907C>T | synonymous_variant | 0.2 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673558 | p.His40Arg | missense_variant | 0.4 |
inhA | 1673602 | c.-600C>T | upstream_gene_variant | 0.12 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 |
inhA | 1674724 | p.Val175Met | missense_variant | 0.12 |
rpsA | 1833779 | p.Val80Leu | missense_variant | 1.0 |
tlyA | 1917937 | c.-3G>A | upstream_gene_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918216 | p.Thr93Ser | missense_variant | 0.2 |
tlyA | 1918366 | p.Ala143Pro | missense_variant | 0.15 |
ndh | 2102412 | p.Val211Met | missense_variant | 0.25 |
ndh | 2102429 | p.Asp205Ala | missense_variant | 0.27 |
ndh | 2102430 | c.612_613insA | frameshift_variant | 0.2 |
ndh | 2102440 | c.603C>T | synonymous_variant | 0.17 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155281 | c.831C>A | synonymous_variant | 0.22 |
katG | 2155407 | c.705G>C | synonymous_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170476 | p.Gly46Asp | missense_variant | 0.2 |
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 | 1.0 |
kasA | 2518588 | c.474T>C | synonymous_variant | 0.11 |
kasA | 2518897 | c.783G>A | synonymous_variant | 0.13 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
eis | 2714781 | c.552G>A | synonymous_variant | 0.5 |
eis | 2714794 | p.Glu180Gly | missense_variant | 0.4 |
eis | 2714980 | p.Leu118Pro | missense_variant | 0.18 |
eis | 2715179 | p.Ala52Pro | missense_variant | 0.12 |
ahpC | 2726017 | c.-176C>T | upstream_gene_variant | 0.14 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2746167 | p.Ala478Thr | missense_variant | 0.12 |
folC | 2746934 | p.Arg222Gln | missense_variant | 0.33 |
folC | 2747340 | p.Thr87Ala | missense_variant | 0.25 |
folC | 2747472 | c.125_126delGC | frameshift_variant | 0.13 |
folC | 2747779 | c.-181G>A | upstream_gene_variant | 0.5 |
pepQ | 2859694 | p.Ala242Val | missense_variant | 0.14 |
ribD | 2987106 | p.Ile90Val | missense_variant | 0.12 |
Rv2752c | 3064672 | p.Ala507Gly | missense_variant | 0.12 |
Rv2752c | 3064709 | p.Arg495Trp | missense_variant | 0.15 |
Rv2752c | 3066320 | c.-129A>G | upstream_gene_variant | 0.2 |
thyX | 3067229 | c.717C>T | synonymous_variant | 0.67 |
thyX | 3067336 | p.Ala204Pro | missense_variant | 0.12 |
thyX | 3067595 | c.351C>T | synonymous_variant | 0.14 |
thyX | 3067913 | c.33G>C | synonymous_variant | 0.29 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086997 | p.Thr60Gly | missense_variant | 0.29 |
ald | 3087805 | p.Trp329* | stop_gained | 0.17 |
fbiD | 3339128 | p.Thr4Ile | missense_variant | 0.12 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
fbiD | 3339556 | p.Gly147Ser | missense_variant | 0.33 |
fbiD | 3339728 | p.Gly204Glu | missense_variant | 0.29 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449052 | c.549C>T | synonymous_variant | 0.14 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3474701 | c.696delC | frameshift_variant | 0.14 |
fprA | 3475039 | p.Gly345Ser | missense_variant | 0.17 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475263 | c.1257G>A | synonymous_variant | 0.13 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
Rv3236c | 3611999 | p.Thr373Cys | missense_variant | 0.17 |
Rv3236c | 3612187 | p.Met310Ile | missense_variant | 0.25 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiB | 3640588 | c.-947C>T | upstream_gene_variant | 0.22 |
fbiB | 3640614 | c.-921C>T | upstream_gene_variant | 0.17 |
fbiA | 3640655 | p.Asp38Ala | missense_variant | 0.14 |
fbiA | 3640829 | p.Gly96Asp | missense_variant | 0.12 |
fbiA | 3640864 | p.Asp108Asn | missense_variant | 0.17 |
fbiB | 3640915 | c.-620C>T | upstream_gene_variant | 0.15 |
fbiA | 3640951 | p.Gln137* | stop_gained | 0.13 |
fbiA | 3641333 | p.Gly264Ala | missense_variant | 0.12 |
fbiA | 3641340 | p.Asp266Glu | missense_variant | 0.12 |
fbiB | 3642134 | c.600G>T | synonymous_variant | 0.2 |
fbiB | 3642396 | p.Ala288Thr | missense_variant | 0.5 |
fbiB | 3642412 | p.Arg293Gln | missense_variant | 0.14 |
fbiB | 3642674 | c.1140C>T | synonymous_variant | 0.25 |
rpoA | 3877850 | p.Gly220Ser | missense_variant | 0.17 |
rpoA | 3878567 | c.-60C>G | upstream_gene_variant | 0.44 |
rpoA | 3878578 | c.-71C>A | upstream_gene_variant | 0.29 |
rpoA | 3878627 | c.-120T>G | upstream_gene_variant | 0.29 |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 0.6 |
clpC1 | 4038222 | p.Ala828Asp | missense_variant | 0.22 |
clpC1 | 4040066 | c.639G>A | synonymous_variant | 0.13 |
clpC1 | 4040233 | p.Arg158Cys | missense_variant | 0.29 |
clpC1 | 4040286 | p.Gln140Arg | missense_variant | 0.22 |
clpC1 | 4040327 | p.Lys126Asn | missense_variant | 0.15 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
panD | 4044477 | c.-196T>C | upstream_gene_variant | 0.33 |
embC | 4239821 | c.-42C>T | upstream_gene_variant | 0.12 |
embC | 4240308 | c.448_449delCC | frameshift_variant | 0.29 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241493 | p.Leu544Pro | missense_variant | 0.14 |
embC | 4241503 | c.1643_1644delTG | frameshift_variant | 0.11 |
embA | 4242430 | c.-803C>G | upstream_gene_variant | 0.29 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243478 | c.246G>A | synonymous_variant | 0.4 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4243763 | c.531G>T | synonymous_variant | 0.17 |
embA | 4243764 | p.Lys178Gln | missense_variant | 0.17 |
embA | 4243772 | c.540A>T | synonymous_variant | 0.17 |
embA | 4243860 | p.Gly210Ser | missense_variant | 0.18 |
embA | 4244184 | p.Ser318Leu | missense_variant | 0.14 |
embA | 4244194 | p.Gly321Ala | missense_variant | 0.11 |
embA | 4244207 | c.975C>T | synonymous_variant | 0.17 |
embA | 4244320 | p.Thr363Ile | missense_variant | 0.13 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4245441 | p.Asp737Asn | missense_variant | 0.14 |
embA | 4245835 | p.Leu868Pro | missense_variant | 0.18 |
embB | 4245842 | c.-672G>T | upstream_gene_variant | 0.15 |
embA | 4245846 | p.Ser872Pro | missense_variant | 0.13 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.4 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.46 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.45 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.45 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.47 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.45 |
embB | 4246591 | c.78G>A | synonymous_variant | 0.13 |
embB | 4246694 | c.181C>A | synonymous_variant | 0.4 |
embB | 4246942 | c.429G>A | synonymous_variant | 0.14 |
embB | 4246953 | p.Arg147His | missense_variant | 0.12 |
embB | 4246959 | p.Glu149Gly | missense_variant | 0.11 |
embB | 4247172 | p.Leu220Gln | missense_variant | 0.5 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4247867 | p.Val452Met | missense_variant | 0.33 |
embB | 4247950 | c.1437G>A | synonymous_variant | 0.14 |
embB | 4248338 | p.Leu609Met | missense_variant | 0.12 |
embB | 4248343 | c.1831delA | frameshift_variant | 0.12 |
aftB | 4268543 | c.294C>T | synonymous_variant | 0.4 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269727 | c.106_107insTG | frameshift_variant | 0.25 |
ubiA | 4269733 | p.Ala34Asp | missense_variant | 0.25 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
ethA | 4327647 | c.-174G>C | upstream_gene_variant | 0.11 |
ethA | 4328413 | c.-940C>T | upstream_gene_variant | 0.22 |
ethA | 4328436 | c.-963G>C | upstream_gene_variant | 1.0 |
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 | 0.93 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4408114 | p.Gly30Val | missense_variant | 0.2 |
gid | 4408122 | c.81G>A | synonymous_variant | 0.18 |