Run ID: ERR4831727
Sample name:
Date: 01-04-2023 21:05:04
Number of reads: 493943
Percentage reads mapped: 94.58
Strain: lineage2.2.2
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 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
inhA | 1674319 | p.Gly40Trp | missense_variant | 0.33 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4248002 | p.Gln497Lys | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5511 | p.Ser91Phe | missense_variant | 0.17 |
gyrB | 5620 | c.381G>A | synonymous_variant | 0.17 |
gyrB | 5643 | p.Leu135Pro | missense_variant | 0.14 |
gyrB | 6179 | p.Gly314Ser | missense_variant | 0.14 |
gyrB | 6530 | p.Ser431Gly | missense_variant | 0.1 |
gyrB | 6873 | p.Leu545Ser | missense_variant | 0.11 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7613 | c.312G>A | synonymous_variant | 1.0 |
gyrA | 8626 | p.Arg442His | missense_variant | 0.13 |
gyrA | 8648 | p.Gln449His | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9806 | p.Gln835His | missense_variant | 0.12 |
fgd1 | 490708 | c.-75G>T | upstream_gene_variant | 0.18 |
fgd1 | 490747 | c.-36C>T | upstream_gene_variant | 0.17 |
fgd1 | 490829 | p.Ala16Glu | missense_variant | 0.29 |
fgd1 | 491213 | p.Ser144Asn | missense_variant | 0.25 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575283 | c.-65C>A | upstream_gene_variant | 0.67 |
mshA | 576088 | p.Phe247Leu | missense_variant | 0.14 |
mshA | 576577 | c.1230C>T | synonymous_variant | 0.18 |
ccsA | 620279 | p.Arg130Leu | missense_variant | 0.12 |
rpoB | 759798 | c.-9G>T | upstream_gene_variant | 0.14 |
rpoB | 760010 | c.204C>T | synonymous_variant | 0.14 |
rpoB | 761579 | c.1773G>A | synonymous_variant | 0.18 |
rpoB | 761861 | c.2055C>T | synonymous_variant | 0.4 |
rpoB | 762182 | p.Asp792Glu | missense_variant | 0.29 |
rpoB | 762783 | p.Asp993Asn | missense_variant | 0.22 |
rpoB | 762946 | p.Thr1047Ile | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763539 | p.Asp57Gly | missense_variant | 0.18 |
rpoC | 764018 | p.Asp217Tyr | missense_variant | 0.33 |
rpoC | 764180 | p.Asp271Tyr | missense_variant | 0.15 |
rpoC | 764347 | c.978G>T | synonymous_variant | 0.14 |
rpoC | 764984 | p.Asp539Tyr | missense_variant | 0.13 |
rpoC | 766663 | c.3294G>T | synonymous_variant | 0.2 |
rpoC | 766682 | p.Val1105Phe | missense_variant | 0.18 |
rpoC | 767253 | p.Pro1295Leu | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776418 | p.Ser688* | stop_gained | 0.29 |
mmpL5 | 776853 | p.Thr543Asn | missense_variant | 0.12 |
mmpL5 | 777010 | p.Pro491Ser | missense_variant | 0.15 |
mmpL5 | 777306 | p.Pro392His | missense_variant | 0.29 |
mmpL5 | 777354 | p.Val376Ala | missense_variant | 0.5 |
mmpL5 | 777596 | c.885G>T | synonymous_variant | 0.15 |
mmpL5 | 777676 | c.805C>T | synonymous_variant | 0.29 |
mmpL5 | 778289 | p.Met64Ile | missense_variant | 0.25 |
mmpL5 | 778348 | p.Val45Ile | missense_variant | 0.18 |
mmpS5 | 778574 | p.Ser111Phe | missense_variant | 0.17 |
mmpR5 | 779128 | p.Asp47Tyr | missense_variant | 0.2 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781857 | p.Gly100Cys | missense_variant | 0.22 |
rplC | 801446 | p.Lys213Ile | missense_variant | 0.12 |
fbiC | 1302970 | p.Ser14Gly | missense_variant | 0.14 |
fbiC | 1303078 | p.Ala50Thr | missense_variant | 0.22 |
fbiC | 1303308 | c.379_381delGAG | conservative_inframe_deletion | 0.2 |
fbiC | 1303427 | p.Gly166Asp | missense_variant | 0.2 |
fbiC | 1303535 | p.Ser202* | stop_gained | 0.17 |
fbiC | 1304444 | p.Ala505Val | missense_variant | 0.25 |
fbiC | 1304493 | p.Asp521Glu | missense_variant | 0.22 |
Rv1258c | 1406145 | p.Ala399Val | missense_variant | 1.0 |
Rv1258c | 1406211 | p.His377Arg | missense_variant | 0.17 |
Rv1258c | 1406869 | p.Pro158Ser | missense_variant | 0.18 |
Rv1258c | 1406956 | p.Pro129Ser | missense_variant | 0.18 |
embR | 1416434 | p.Ala305Val | missense_variant | 0.14 |
embR | 1416708 | p.Ala214Thr | missense_variant | 0.14 |
embR | 1416775 | c.573C>T | synonymous_variant | 0.18 |
embR | 1417044 | p.Arg102Trp | missense_variant | 0.29 |
embR | 1417169 | p.Trp60Leu | missense_variant | 0.17 |
embR | 1417295 | p.Pro18Leu | missense_variant | 0.18 |
atpE | 1461243 | p.Asn67Asp | missense_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471833 | n.-13G>T | upstream_gene_variant | 0.15 |
rrs | 1472276 | n.431A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472374 | n.529T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472766 | n.921G>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473261 | n.1416G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474342 | n.685G>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474974 | n.1317G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475315 | n.1658A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475535 | n.1878G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476125 | n.2468G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476523 | n.2866T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476528 | n.2871A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476539 | n.2882A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476585 | n.2928A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476668 | n.3011C>A | non_coding_transcript_exon_variant | 0.15 |
inhA | 1673796 | c.-406G>T | upstream_gene_variant | 0.18 |
inhA | 1674353 | p.Thr51Ile | missense_variant | 0.17 |
inhA | 1674377 | p.Pro59Gln | missense_variant | 0.18 |
rpsA | 1833529 | c.-13G>T | upstream_gene_variant | 0.18 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834521 | p.Ala327Asp | missense_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918231 | p.Glu98Lys | missense_variant | 0.2 |
ndh | 2102556 | p.Asp163Asn | missense_variant | 0.14 |
ndh | 2102944 | c.99C>T | synonymous_variant | 0.14 |
ndh | 2103009 | p.Pro12Thr | missense_variant | 0.15 |
ndh | 2103220 | c.-178C>A | upstream_gene_variant | 0.12 |
katG | 2154034 | p.Arg693His | missense_variant | 0.17 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154750 | p.Glu454Asp | missense_variant | 0.17 |
katG | 2155375 | p.Val246Ala | missense_variant | 0.33 |
katG | 2155611 | p.Phe167Leu | missense_variant | 0.2 |
katG | 2156091 | c.21C>A | synonymous_variant | 0.18 |
katG | 2156470 | c.-359C>A | upstream_gene_variant | 0.13 |
katG | 2156476 | c.-365G>A | upstream_gene_variant | 0.13 |
PPE35 | 2167877 | p.Ser912Arg | missense_variant | 0.13 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168065 | p.Thr850Ala | missense_variant | 0.2 |
PPE35 | 2169628 | p.Ile329Val | missense_variant | 0.11 |
PPE35 | 2169769 | p.Ala282Thr | missense_variant | 0.25 |
PPE35 | 2169969 | p.Gly215Val | missense_variant | 0.14 |
PPE35 | 2169992 | c.621C>A | synonymous_variant | 0.14 |
Rv1979c | 2222728 | p.Gly146Asp | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288758 | p.Gly162Ser | missense_variant | 0.18 |
pncA | 2288765 | c.477G>A | synonymous_variant | 0.15 |
pncA | 2289175 | p.Gly23Ser | missense_variant | 0.2 |
pncA | 2289565 | c.-324G>A | upstream_gene_variant | 0.17 |
pncA | 2289961 | c.-720C>A | upstream_gene_variant | 0.17 |
kasA | 2518411 | c.297C>T | synonymous_variant | 0.4 |
kasA | 2518956 | p.Ala281Glu | missense_variant | 0.15 |
kasA | 2519213 | p.Ile367Phe | missense_variant | 1.0 |
eis | 2714427 | c.906G>A | synonymous_variant | 0.18 |
eis | 2714438 | p.Met299Val | missense_variant | 0.13 |
eis | 2714709 | c.624C>T | synonymous_variant | 0.18 |
eis | 2714816 | p.Gly173Ser | missense_variant | 0.22 |
eis | 2714935 | p.Pro133Leu | missense_variant | 0.22 |
eis | 2714967 | c.366G>A | synonymous_variant | 0.25 |
eis | 2714983 | p.Ala117Glu | missense_variant | 0.25 |
eis | 2715392 | c.-60G>T | upstream_gene_variant | 0.15 |
eis | 2715568 | c.-236G>A | upstream_gene_variant | 0.17 |
ahpC | 2726293 | p.Tyr34Cys | missense_variant | 0.13 |
ahpC | 2726553 | p.Ala121Thr | missense_variant | 0.14 |
ahpC | 2726571 | p.Ala127Thr | missense_variant | 0.15 |
folC | 2746411 | c.1188G>A | synonymous_variant | 0.5 |
folC | 2747251 | p.Ser116Arg | missense_variant | 0.15 |
folC | 2747352 | p.Asp83Tyr | missense_variant | 0.2 |
pepQ | 2859732 | p.Tyr229* | stop_gained | 0.15 |
pepQ | 2860074 | p.Glu115Asp | missense_variant | 0.15 |
pepQ | 2860287 | c.132G>T | synonymous_variant | 0.12 |
ribD | 2986868 | c.30T>C | synonymous_variant | 0.12 |
ribD | 2987213 | c.375C>A | synonymous_variant | 0.2 |
ribD | 2987533 | p.Gly232Glu | missense_variant | 0.17 |
Rv2752c | 3065231 | p.Gly321Trp | missense_variant | 0.14 |
Rv2752c | 3065507 | p.Ala229Ser | missense_variant | 0.17 |
Rv2752c | 3066173 | p.Pro7Thr | missense_variant | 0.17 |
Rv2752c | 3066232 | c.-41T>C | upstream_gene_variant | 0.11 |
Rv2752c | 3066288 | c.-97G>A | upstream_gene_variant | 0.15 |
thyA | 3073890 | p.Leu194Phe | missense_variant | 0.15 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087024 | c.206delA | frameshift_variant | 0.29 |
ald | 3087110 | c.291G>A | synonymous_variant | 0.18 |
ald | 3087189 | p.Asp124Tyr | missense_variant | 0.14 |
fbiD | 3339199 | p.Pro28Thr | missense_variant | 0.67 |
fbiD | 3339646 | p.Glu177Lys | missense_variant | 0.5 |
Rv3083 | 3448819 | p.Thr106Ser | missense_variant | 0.15 |
Rv3083 | 3449253 | c.750C>A | synonymous_variant | 0.14 |
Rv3083 | 3449924 | p.Leu474Pro | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474024 | c.18C>T | synonymous_variant | 0.2 |
fprA | 3474169 | p.Pro55Ser | missense_variant | 0.2 |
fprA | 3474610 | p.Pro202Thr | missense_variant | 0.29 |
fprA | 3474903 | c.897C>T | synonymous_variant | 0.14 |
fprA | 3475376 | c.1370G>A | splice_region_variant&stop_retained_variant | 0.22 |
whiB7 | 3568670 | c.10C>T | synonymous_variant | 0.17 |
whiB7 | 3568737 | c.-58C>A | upstream_gene_variant | 0.25 |
Rv3236c | 3612545 | p.Ala191Asp | missense_variant | 0.18 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3613100 | p.Ala6Val | missense_variant | 0.15 |
fbiA | 3640981 | p.Asp147Asn | missense_variant | 0.14 |
fbiA | 3641472 | p.Met310Ile | missense_variant | 0.25 |
fbiB | 3641523 | c.-12G>C | upstream_gene_variant | 0.13 |
fbiB | 3641543 | c.9C>A | synonymous_variant | 0.18 |
fbiB | 3642621 | p.Ala363Ser | missense_variant | 0.13 |
fbiB | 3642635 | p.Asp367Glu | missense_variant | 0.15 |
alr | 3840654 | p.Ala256Val | missense_variant | 0.12 |
alr | 3840798 | p.Asn208Ser | missense_variant | 0.1 |
rpoA | 3877805 | p.Gly235Trp | missense_variant | 0.14 |
rpoA | 3878241 | p.Glu89Asp | missense_variant | 0.11 |
rpoA | 3878418 | c.90C>T | synonymous_variant | 0.17 |
clpC1 | 4038338 | c.2367C>A | synonymous_variant | 0.18 |
clpC1 | 4038728 | c.1977C>T | synonymous_variant | 0.14 |
clpC1 | 4038851 | c.1854G>A | synonymous_variant | 0.29 |
clpC1 | 4038863 | c.1842G>T | synonymous_variant | 0.29 |
clpC1 | 4039204 | p.Glu501Lys | missense_variant | 0.15 |
clpC1 | 4039697 | c.1008C>T | synonymous_variant | 0.2 |
clpC1 | 4039820 | c.885T>C | synonymous_variant | 0.14 |
clpC1 | 4040014 | p.Gln231* | stop_gained | 0.15 |
clpC1 | 4040539 | p.Leu56Met | missense_variant | 0.13 |
panD | 4043917 | p.Ala122Glu | missense_variant | 0.12 |
embC | 4239921 | p.Arg20Leu | missense_variant | 0.12 |
embC | 4239951 | p.Arg30Gln | missense_variant | 0.13 |
embC | 4240680 | p.Leu273Pro | missense_variant | 0.25 |
embC | 4241549 | p.Gly563Arg | missense_variant | 0.18 |
embC | 4241605 | c.1743C>T | synonymous_variant | 0.18 |
embC | 4241644 | c.1782G>A | synonymous_variant | 0.17 |
embC | 4241692 | c.1830C>T | synonymous_variant | 0.22 |
embC | 4241744 | p.Phe628Leu | missense_variant | 0.17 |
embC | 4241999 | p.Trp713Arg | missense_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242869 | p.Val1003Ile | missense_variant | 0.2 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243526 | c.294G>A | synonymous_variant | 0.15 |
embA | 4243557 | p.Ala109Ser | missense_variant | 0.25 |
embA | 4243716 | p.Leu162Met | missense_variant | 0.29 |
embA | 4244007 | p.Ala259Thr | missense_variant | 0.29 |
embB | 4245827 | c.-687C>T | upstream_gene_variant | 0.29 |
embB | 4247131 | c.618C>A | synonymous_variant | 0.29 |
embB | 4247171 | p.Leu220Val | missense_variant | 0.22 |
embB | 4247667 | p.Trp385Leu | missense_variant | 0.25 |
embB | 4248795 | p.Ala761Gly | missense_variant | 0.13 |
embB | 4249312 | c.2799C>A | synonymous_variant | 0.22 |
embB | 4249424 | c.2911C>T | synonymous_variant | 0.17 |
aftB | 4267073 | c.1764C>A | synonymous_variant | 0.18 |
aftB | 4267222 | p.Ala539Ser | missense_variant | 0.13 |
aftB | 4267494 | p.Gly448Val | missense_variant | 0.12 |
aftB | 4267591 | p.Gln416* | stop_gained | 0.2 |
aftB | 4267593 | p.Ala415Asp | missense_variant | 0.2 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ubiA | 4269046 | p.Ala263Val | missense_variant | 0.2 |
ubiA | 4269068 | p.Thr256Ala | missense_variant | 0.2 |
aftB | 4269666 | c.-830G>T | upstream_gene_variant | 0.18 |
aftB | 4269737 | c.-901C>T | upstream_gene_variant | 0.11 |
ethA | 4326013 | c.1461G>T | synonymous_variant | 0.15 |
ethA | 4326039 | p.Arg479Trp | missense_variant | 0.12 |
ethA | 4326130 | c.1344G>A | synonymous_variant | 1.0 |
ethA | 4327058 | p.Gly139Asp | missense_variant | 0.85 |
ethA | 4327149 | p.Trp109Arg | missense_variant | 0.12 |
ethR | 4327841 | p.Asp98Gly | missense_variant | 0.14 |
ethR | 4328110 | p.Ala188Ser | missense_variant | 0.13 |
ethR | 4328147 | p.Leu200Pro | missense_variant | 0.11 |
ethA | 4328445 | c.-972A>G | upstream_gene_variant | 0.29 |
whiB6 | 4338208 | p.Pro105Gln | missense_variant | 0.17 |
whiB6 | 4338358 | p.Ala55Asp | missense_variant | 0.17 |
whiB6 | 4338577 | c.-56G>A | upstream_gene_variant | 0.13 |
whiB6 | 4338579 | c.-58C>G | upstream_gene_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407704 | p.Ala167Ser | missense_variant | 0.33 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
gid | 4408062 | c.141G>A | synonymous_variant | 0.2 |
gid | 4408235 | c.-33T>G | upstream_gene_variant | 0.17 |
gid | 4408264 | c.-62C>T | upstream_gene_variant | 0.18 |
gid | 4408379 | c.-177C>A | upstream_gene_variant | 0.4 |