Run ID: SRR11972164
Sample name:
Date: 03-04-2023 05:30:39
Number of reads: 598500
Percentage reads mapped: 99.14
Strain: lineage2.2.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288697 | p.Leu182Ser | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.5 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9564 | p.Tyr755Asn | missense_variant | 0.4 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575746 | c.399C>T | synonymous_variant | 0.22 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 762248 | c.2442G>C | synonymous_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765822 | p.Ala818Val | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775864 | p.Ala873Ser | missense_variant | 0.15 |
mmpL5 | 775865 | c.2616T>G | synonymous_variant | 0.15 |
mmpL5 | 775927 | c.2554C>T | synonymous_variant | 0.2 |
mmpL5 | 775931 | c.2550C>T | synonymous_variant | 0.25 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpL5 | 778956 | c.-476G>C | upstream_gene_variant | 0.15 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303005 | c.75G>T | synonymous_variant | 0.22 |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.27 |
fbiC | 1303107 | c.177C>T | synonymous_variant | 0.29 |
fbiC | 1304293 | p.Thr455Ala | missense_variant | 0.29 |
fbiC | 1305316 | c.2389delC | frameshift_variant | 0.15 |
Rv1258c | 1406299 | p.Val348Ile | missense_variant | 0.14 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472193 | n.348A>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.66 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.68 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472350 | n.505C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472373 | n.528G>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.18 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.22 |
fabG1 | 1674085 | p.Glu216Lys | missense_variant | 0.29 |
rpsA | 1833558 | p.Val6Asp | missense_variant | 0.14 |
rpsA | 1833565 | c.24G>C | synonymous_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834292 | c.752delT | frameshift_variant | 0.2 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102392 | c.650_651insA | frameshift_variant | 0.22 |
ndh | 2102968 | c.75C>T | synonymous_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.15 |
PPE35 | 2167898 | c.2715G>C | synonymous_variant | 0.12 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.13 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.17 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.38 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.38 |
PPE35 | 2170171 | p.Val148Ile | missense_variant | 0.12 |
PPE35 | 2170238 | c.375T>G | synonymous_variant | 0.17 |
Rv1979c | 2222949 | c.216C>A | synonymous_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289705 | c.-464G>T | upstream_gene_variant | 0.2 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.29 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.33 |
eis | 2714846 | p.Val163Ile | missense_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.25 |
ahpC | 2726350 | p.Trp53Leu | missense_variant | 0.2 |
ahpC | 2726456 | c.264C>T | synonymous_variant | 0.17 |
thyA | 3074653 | c.-182G>A | upstream_gene_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448402 | c.-102C>T | upstream_gene_variant | 0.25 |
Rv3083 | 3448641 | c.138C>T | synonymous_variant | 0.18 |
Rv3083 | 3448650 | c.147C>T | synonymous_variant | 0.18 |
Rv3083 | 3448653 | c.150C>T | synonymous_variant | 0.18 |
Rv3083 | 3448656 | c.153G>C | synonymous_variant | 0.18 |
Rv3083 | 3448660 | p.Val53Ile | missense_variant | 0.18 |
Rv3083 | 3448665 | c.162T>C | synonymous_variant | 0.22 |
Rv3083 | 3448668 | c.165G>C | synonymous_variant | 0.22 |
Rv3083 | 3448859 | p.Ala119Glu | missense_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474143 | p.Trp46Tyr | missense_variant | 0.25 |
fprA | 3474708 | c.702C>T | synonymous_variant | 0.5 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
alr | 3841203 | p.Gly73Val | missense_variant | 0.22 |
ddn | 3987019 | p.Pro59Leu | missense_variant | 0.33 |
ddn | 3987060 | p.Val73Ile | missense_variant | 0.29 |
clpC1 | 4039645 | p.His354Asp | missense_variant | 0.24 |
clpC1 | 4039730 | c.975C>G | synonymous_variant | 0.15 |
clpC1 | 4039829 | p.Leu292Ile | missense_variant | 0.18 |
embC | 4239854 | c.-9G>T | upstream_gene_variant | 0.2 |
embC | 4240655 | p.Ala265Pro | missense_variant | 0.4 |
embC | 4240801 | c.939C>T | synonymous_variant | 0.38 |
embC | 4240803 | p.Tyr314Phe | missense_variant | 0.38 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245330 | p.Gly700Ser | missense_variant | 0.14 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.33 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.33 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.33 |
embB | 4247426 | p.Gly305Thr | missense_variant | 0.4 |
embB | 4248115 | c.1602C>T | synonymous_variant | 1.0 |
embB | 4248500 | p.Ile663Val | missense_variant | 0.15 |
embB | 4248803 | p.Met764Val | missense_variant | 0.33 |
embB | 4248977 | p.Thr822Ala | missense_variant | 0.33 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268622 | p.Trp72* | stop_gained | 0.25 |
ubiA | 4269265 | p.Gly190Asp | missense_variant | 0.22 |
aftB | 4269702 | c.-866C>A | upstream_gene_variant | 0.25 |
ubiA | 4269791 | p.Ala15Thr | missense_variant | 0.29 |
ubiA | 4269794 | p.Val14Phe | missense_variant | 0.29 |
ethA | 4328366 | c.-893G>A | upstream_gene_variant | 0.18 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
gid | 4408124 | p.Ala27Ser | missense_variant | 0.25 |