Run ID: ERR6336804
Sample name:
Date: 02-04-2023 02:04:00
Number of reads: 618038
Percentage reads mapped: 98.92
Strain: lineage1.2.1.2
Drug-resistance: HR-TB
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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2153909 | p.Asp735Asn | missense_variant | 0.2 | isoniazid |
gid | 4407796 | p.Ser136* | stop_gained | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5669 | p.Tyr144His | missense_variant | 0.12 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 6622 | c.-680C>T | upstream_gene_variant | 0.13 |
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 | 9260 | c.1959G>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9513 | p.Glu738Lys | missense_variant | 0.18 |
gyrA | 9606 | p.Asp769Asn | missense_variant | 0.12 |
fgd1 | 491005 | c.223C>T | synonymous_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575327 | c.-21G>A | upstream_gene_variant | 0.22 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 575391 | p.Gln15Arg | missense_variant | 0.25 |
mshA | 576007 | c.660A>G | synonymous_variant | 0.11 |
ccsA | 619762 | c.-129C>T | upstream_gene_variant | 0.29 |
ccsA | 619940 | p.Ala17Val | missense_variant | 0.13 |
ccsA | 620558 | p.Gln223Arg | missense_variant | 0.11 |
ccsA | 620698 | p.Val270Ile | missense_variant | 0.15 |
rpoB | 760045 | p.Leu80Gln | missense_variant | 0.15 |
rpoB | 761451 | p.Val549Phe | missense_variant | 0.14 |
rpoB | 761605 | p.Leu600Pro | missense_variant | 0.14 |
rpoB | 761610 | p.Gly602Arg | missense_variant | 0.17 |
rpoB | 761652 | p.Glu616Lys | missense_variant | 0.13 |
rpoB | 761814 | p.Ala670Thr | missense_variant | 0.18 |
rpoB | 762097 | p.Thr764Ser | missense_variant | 0.13 |
rpoB | 762116 | c.2310C>T | synonymous_variant | 0.22 |
rpoB | 762293 | c.2487T>A | synonymous_variant | 0.14 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763342 | c.-28C>T | upstream_gene_variant | 0.12 |
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 | 764548 | c.1179G>A | synonymous_variant | 0.2 |
rpoC | 765391 | c.2022C>T | synonymous_variant | 0.17 |
rpoC | 765523 | c.2154C>T | synonymous_variant | 0.15 |
rpoC | 765557 | p.Thr730Ser | missense_variant | 0.17 |
rpoC | 767022 | p.Asp1218Gly | missense_variant | 0.17 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777255 | p.Pro409Leu | missense_variant | 0.17 |
mmpL5 | 778033 | p.Gln150* | stop_gained | 0.13 |
mmpL5 | 778210 | p.Ala91Thr | missense_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781647 | p.Arg30Cys | missense_variant | 0.15 |
rplC | 801359 | p.Lys184Arg | missense_variant | 0.11 |
fbiC | 1302870 | c.-61G>A | upstream_gene_variant | 0.17 |
fbiC | 1304159 | p.Val410Ala | missense_variant | 0.11 |
fbiC | 1304313 | c.1383A>G | synonymous_variant | 0.13 |
fbiC | 1304817 | c.1887T>C | synonymous_variant | 0.14 |
Rv1258c | 1406531 | c.810C>T | synonymous_variant | 0.22 |
Rv1258c | 1407092 | c.249T>C | synonymous_variant | 0.12 |
embR | 1416915 | p.Trp145Gly | missense_variant | 0.25 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
embR | 1417038 | p.Ser104Gly | missense_variant | 0.15 |
embR | 1417049 | p.Gly100Asp | missense_variant | 0.18 |
embR | 1417063 | c.285C>A | synonymous_variant | 0.2 |
embR | 1417087 | c.261G>T | synonymous_variant | 0.2 |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472753 | n.908A>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1474468 | n.811G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474732 | n.1075A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476196 | n.2539C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.12 |
fabG1 | 1673755 | p.Glu106Lys | missense_variant | 0.12 |
inhA | 1674300 | c.99C>T | synonymous_variant | 0.12 |
inhA | 1674484 | p.Ile95Leu | missense_variant | 1.0 |
rpsA | 1833380 | c.-162G>A | upstream_gene_variant | 0.18 |
rpsA | 1834896 | p.Ser452Thr | missense_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102372 | p.Met224Thr | missense_variant | 0.29 |
ndh | 2102379 | c.663delG | frameshift_variant | 0.17 |
katG | 2154494 | p.Phe540Leu | missense_variant | 0.12 |
katG | 2154495 | c.1617C>T | synonymous_variant | 0.12 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155772 | p.Arg114Cys | missense_variant | 0.2 |
katG | 2155914 | c.198G>A | synonymous_variant | 0.15 |
PPE35 | 2167861 | p.Gly918Cys | missense_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168464 | p.Pro717Ser | missense_variant | 0.17 |
PPE35 | 2169022 | p.Gly531Arg | missense_variant | 0.14 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.29 |
Rv1979c | 2222214 | c.951C>G | synonymous_variant | 0.15 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2222625 | c.540C>T | synonymous_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289133 | p.Glu37Lys | missense_variant | 0.15 |
pncA | 2290095 | c.-854C>T | upstream_gene_variant | 0.17 |
kasA | 2518103 | c.-12G>A | upstream_gene_variant | 0.14 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
kasA | 2518302 | p.His63Leu | missense_variant | 0.13 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
kasA | 2519071 | c.957C>T | synonymous_variant | 0.14 |
kasA | 2519335 | c.1221C>T | synonymous_variant | 0.22 |
eis | 2714340 | c.993C>T | synonymous_variant | 0.15 |
eis | 2715278 | c.55C>T | synonymous_variant | 0.12 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726466 | p.Ala92Thr | missense_variant | 0.13 |
folC | 2747565 | p.Gly12Arg | missense_variant | 0.12 |
Rv2752c | 3065305 | p.Ala296Val | missense_variant | 0.18 |
thyX | 3067246 | c.699delC | frameshift_variant | 0.33 |
thyX | 3067929 | p.Pro6Leu | missense_variant | 0.33 |
thyA | 3074575 | c.-105delC | upstream_gene_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087446 | c.627C>A | synonymous_variant | 0.14 |
ald | 3087716 | c.897G>A | synonymous_variant | 0.13 |
ald | 3087769 | p.Thr317Met | missense_variant | 0.18 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
fbiD | 3339431 | p.Glu105Ala | missense_variant | 0.12 |
fbiD | 3339741 | c.624G>T | synonymous_variant | 0.4 |
fbiD | 3339744 | c.627A>C | synonymous_variant | 0.4 |
Rv3083 | 3448701 | c.198C>T | synonymous_variant | 0.14 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449569 | p.Met356Val | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3474850 | p.Arg282Cys | missense_variant | 0.13 |
fprA | 3474970 | p.Val322Ile | missense_variant | 0.12 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
whiB7 | 3568666 | p.Thr5Lys | missense_variant | 0.13 |
whiB7 | 3568711 | c.-32G>A | upstream_gene_variant | 0.12 |
Rv3236c | 3611984 | p.Pro378Leu | missense_variant | 0.13 |
Rv3236c | 3612076 | c.1041G>A | synonymous_variant | 0.12 |
Rv3236c | 3612091 | c.1026G>C | synonymous_variant | 0.11 |
Rv3236c | 3612422 | p.Val232Ala | missense_variant | 0.14 |
Rv3236c | 3612450 | p.Leu223Val | missense_variant | 0.13 |
Rv3236c | 3612573 | p.Val182Leu | missense_variant | 0.12 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiA | 3640592 | p.Leu17Arg | missense_variant | 0.12 |
fbiB | 3640599 | c.-936C>G | upstream_gene_variant | 0.13 |
fbiA | 3641104 | p.Val188Phe | missense_variant | 1.0 |
fbiB | 3642033 | p.Ala167Thr | missense_variant | 0.18 |
fbiB | 3642143 | c.609C>T | synonymous_variant | 0.14 |
alr | 3841225 | p.Lys66Glu | missense_variant | 0.14 |
alr | 3841574 | c.-154T>C | upstream_gene_variant | 0.12 |
rpoA | 3877954 | p.Gln185Arg | missense_variant | 0.12 |
rpoA | 3877968 | c.540C>T | synonymous_variant | 0.17 |
rpoA | 3878202 | c.306G>A | synonymous_variant | 0.15 |
ddn | 3986659 | c.-185A>C | upstream_gene_variant | 0.13 |
ddn | 3986928 | p.Tyr29His | missense_variant | 0.12 |
clpC1 | 4038579 | p.Phe709Ser | missense_variant | 0.11 |
clpC1 | 4040247 | p.Ala153Val | missense_variant | 0.12 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239790 | c.-73C>T | upstream_gene_variant | 0.14 |
embC | 4240103 | p.Asp81Asn | missense_variant | 0.13 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4240693 | c.831T>C | synonymous_variant | 0.15 |
embC | 4240803 | p.Tyr314Cys | missense_variant | 0.17 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241452 | c.1590G>A | synonymous_variant | 0.18 |
embC | 4241878 | c.2016G>C | synonymous_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242770 | p.Thr970Ala | missense_variant | 0.11 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4243848 | p.Val206Leu | missense_variant | 0.25 |
embA | 4243945 | p.Thr238Ile | missense_variant | 0.13 |
embA | 4244184 | p.Ser318Leu | missense_variant | 0.2 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embB | 4246615 | c.102G>A | synonymous_variant | 0.4 |
embB | 4246811 | p.Gly100Ser | missense_variant | 0.12 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4247916 | p.Arg468His | missense_variant | 0.14 |
embB | 4248325 | c.1812G>A | synonymous_variant | 0.2 |
aftB | 4267926 | c.910delG | frameshift_variant | 0.2 |
aftB | 4268622 | p.Trp72Ser | missense_variant | 0.17 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269603 | c.-767C>T | upstream_gene_variant | 0.14 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ethA | 4326428 | p.Phe349Ser | missense_variant | 0.17 |
ethA | 4326921 | p.Ala185Thr | missense_variant | 0.2 |
ethR | 4328144 | p.Val199Ala | missense_variant | 0.13 |
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 | 4407792 | c.411G>A | synonymous_variant | 0.15 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4408361 | c.-159A>C | upstream_gene_variant | 0.14 |