Run ID: SRR5817480
Sample name:
Date: 04-04-2023 11:13:23
Number of reads: 581924
Percentage reads mapped: 99.22
Strain:
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
lineage1.2.1.2 | Indo-Oceanic | NA | RD239 | 0.98 |
lineage1.2.1.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrB | 6382 | p.Lys381Asn | missense_variant | 0.4 |
gyrB | 7158 | c.1931_1933delCCG | disruptive_inframe_deletion | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7411 | p.Val37Gly | missense_variant | 0.23 |
gyrA | 7444 | p.Leu48Arg | missense_variant | 0.38 |
gyrA | 7527 | p.Ser76Ala | missense_variant | 0.31 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7684 | p.Arg128Met | missense_variant | 0.4 |
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 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
fgd1 | 491769 | c.987A>G | synonymous_variant | 0.15 |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 |
mshA | 575420 | p.Thr25Pro | missense_variant | 0.21 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.27 |
mshA | 576123 | p.Leu259Arg | missense_variant | 0.38 |
mshA | 576180 | p.Lys278Met | missense_variant | 0.33 |
ccsA | 619787 | c.-104T>G | upstream_gene_variant | 0.18 |
ccsA | 619958 | p.Val23Gly | missense_variant | 0.29 |
ccsA | 620047 | p.Ser53Ala | missense_variant | 0.33 |
ccsA | 620159 | p.Leu90Arg | missense_variant | 0.2 |
rpoB | 760504 | p.Lys233Met | missense_variant | 0.22 |
rpoB | 761883 | p.Gly693Cys | missense_variant | 0.17 |
rpoB | 762293 | c.2487T>A | synonymous_variant | 0.17 |
rpoB | 762682 | p.Glu959Ala | missense_variant | 0.38 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763207 | p.Ser1134Ile | missense_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 | 764327 | p.Ile320Leu | missense_variant | 0.62 |
rpoC | 765717 | p.Asp783Ala | missense_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775682 | c.2799C>A | synonymous_variant | 0.22 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776128 | p.Cys785Ser | missense_variant | 0.17 |
mmpL5 | 776329 | p.Phe718Val | missense_variant | 0.33 |
mmpL5 | 776712 | p.His590Leu | missense_variant | 0.14 |
mmpL5 | 776776 | p.Asn569Tyr | missense_variant | 0.4 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.93 |
rpsL | 781798 | p.Val80Gly | missense_variant | 0.22 |
fbiC | 1303726 | p.Thr266Pro | missense_variant | 0.22 |
fbiC | 1305023 | p.His698Leu | missense_variant | 0.23 |
fbiC | 1305058 | p.Tyr710Asp | missense_variant | 0.14 |
Rv1258c | 1406127 | p.Leu405Gln | missense_variant | 0.29 |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 |
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 | 1.0 |
rrs | 1472079 | n.234C>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472759 | n.914T>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472804 | n.959G>T | non_coding_transcript_exon_variant | 0.29 |
fabG1 | 1673388 | c.-52T>G | upstream_gene_variant | 0.21 |
fabG1 | 1673561 | p.Lys41Met | missense_variant | 0.13 |
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 |
inhA | 1674870 | p.Asp223Glu | missense_variant | 0.38 |
rpsA | 1833949 | c.408T>C | synonymous_variant | 0.2 |
tlyA | 1917826 | c.-114A>C | upstream_gene_variant | 0.38 |
tlyA | 1917835 | c.-105A>C | upstream_gene_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918168 | p.Phe77Val | missense_variant | 0.15 |
tlyA | 1918621 | p.Ser228Cys | missense_variant | 0.31 |
ndh | 2102337 | p.Leu236Val | missense_variant | 0.13 |
ndh | 2103150 | c.-108T>G | upstream_gene_variant | 0.25 |
ndh | 2103194 | c.-152T>G | upstream_gene_variant | 0.18 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155358 | p.Phe252Val | missense_variant | 0.33 |
katG | 2155735 | p.Met126Lys | missense_variant | 0.25 |
katG | 2155997 | p.Trp39Gly | missense_variant | 0.2 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2169190 | p.Phe475Ile | missense_variant | 0.27 |
PPE35 | 2169976 | p.Gly213Ser | missense_variant | 0.12 |
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 | 2519048 | p.Gly312Ser | missense_variant | 1.0 |
eis | 2714191 | p.Gln381Leu | missense_variant | 0.27 |
eis | 2714236 | p.Ala366Val | missense_variant | 0.33 |
eis | 2714247 | c.1086A>T | synonymous_variant | 0.5 |
eis | 2714832 | p.Arg167Ser | missense_variant | 0.38 |
ahpC | 2726001 | c.-192T>C | upstream_gene_variant | 0.12 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
ahpC | 2726140 | c.-53A>G | upstream_gene_variant | 0.13 |
ahpC | 2726731 | p.Lys180Met | missense_variant | 0.21 |
folC | 2746457 | p.Val381Gly | missense_variant | 0.3 |
folC | 2747036 | p.Asn188Thr | missense_variant | 0.33 |
folC | 2747559 | p.Ala14Thr | missense_variant | 0.17 |
folC | 2747691 | c.-93A>C | upstream_gene_variant | 0.2 |
pepQ | 2859558 | c.861C>T | synonymous_variant | 0.18 |
pepQ | 2859625 | p.Leu265Arg | missense_variant | 0.38 |
pepQ | 2860466 | c.-48C>T | upstream_gene_variant | 0.13 |
ribD | 2987266 | p.Leu143Arg | missense_variant | 0.36 |
Rv2752c | 3064528 | p.Val555Gly | missense_variant | 0.33 |
Rv2752c | 3064543 | p.Met550Arg | missense_variant | 0.22 |
Rv2752c | 3065638 | p.Leu185Gln | missense_variant | 0.25 |
Rv2752c | 3065836 | p.Tyr119Cys | missense_variant | 0.14 |
Rv2752c | 3066085 | p.His36Arg | missense_variant | 0.22 |
thyX | 3067551 | p.Leu132Gln | missense_variant | 0.2 |
thyA | 3074364 | p.Tyr36* | stop_gained | 0.33 |
thyA | 3074492 | c.-21T>G | upstream_gene_variant | 0.31 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 |
fbiD | 3339548 | p.Leu144His | missense_variant | 0.3 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449035 | p.Lys178* | stop_gained | 0.29 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474057 | c.51C>T | synonymous_variant | 0.22 |
fprA | 3474074 | p.Leu23Arg | missense_variant | 0.22 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475273 | p.Trp423Arg | missense_variant | 0.38 |
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 |
whiB7 | 3568622 | p.Cys20Gly | missense_variant | 0.18 |
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 |
fbiA | 3640924 | p.Ile128Leu | missense_variant | 0.2 |
fbiB | 3642087 | p.Asn185Tyr | missense_variant | 0.2 |
fbiB | 3642336 | p.Thr268Pro | missense_variant | 0.15 |
fbiB | 3642483 | p.Trp317Arg | missense_variant | 0.17 |
fbiB | 3642562 | p.Asp343Ala | missense_variant | 0.25 |
alr | 3840476 | c.945A>T | synonymous_variant | 0.25 |
rpoA | 3878091 | c.417C>T | synonymous_variant | 0.18 |
clpC1 | 4038599 | c.2106G>A | synonymous_variant | 1.0 |
clpC1 | 4040209 | p.Ser166Ala | missense_variant | 0.2 |
clpC1 | 4040249 | p.Glu152Ala | missense_variant | 0.31 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
embC | 4239883 | c.21A>G | synonymous_variant | 0.25 |
embC | 4240025 | p.Thr55Pro | missense_variant | 0.22 |
embC | 4240281 | p.Val140Gly | missense_variant | 0.33 |
embC | 4240583 | p.Thr241Pro | missense_variant | 0.4 |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242995 | p.Val1045Leu | missense_variant | 0.14 |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 |
embA | 4245541 | p.Val770Gly | missense_variant | 0.33 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246329 | p.Thr1033Ser | missense_variant | 0.25 |
embB | 4246529 | p.Ser6Arg | missense_variant | 0.33 |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249470 | p.Leu986Arg | missense_variant | 0.4 |
embB | 4249574 | p.Lys1021* | stop_gained | 0.18 |
aftB | 4267386 | p.His484Leu | missense_variant | 0.29 |
aftB | 4268807 | c.30G>T | synonymous_variant | 0.67 |
ubiA | 4268959 | p.Ile292Thr | missense_variant | 0.29 |
ubiA | 4269218 | p.Ile206Leu | missense_variant | 0.29 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
ubiA | 4269754 | p.Val27Ala | missense_variant | 0.17 |
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 |
ethA | 4326083 | p.Asp464Ala | missense_variant | 0.33 |
ethA | 4326161 | p.Tyr438Phe | missense_variant | 0.33 |
ethA | 4327146 | p.Ser110Ala | missense_variant | 0.13 |
ethA | 4327225 | p.Glu83Asp | missense_variant | 0.17 |
ethR | 4328151 | p.Asp201Glu | missense_variant | 0.2 |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 1.0 |
whiB6 | 4338520 | c.2T>C | start_lost | 0.94 |
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 | 4407873 | c.330G>T | synonymous_variant | 1.0 |