Run ID: ERR3077966
Sample name:
Date: 01-04-2023 00:12:56
Number of reads: 577267
Percentage reads mapped: 99.26
Strain: lineage3.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
lineage3.1.1 | East-African-Indian | CAS1-Kili | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 0.15 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.8 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.75 | isoniazid |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.13 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5101 | c.-139G>T | upstream_gene_variant | 0.12 |
gyrB | 5620 | c.381G>T | synonymous_variant | 0.12 |
gyrB | 5861 | c.622C>T | synonymous_variant | 0.13 |
gyrA | 7018 | c.-284G>T | upstream_gene_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7563 | p.Gly88Ser | missense_variant | 0.17 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7605 | p.Pro102Ala | missense_variant | 0.14 |
gyrA | 8445 | p.Arg382Ser | missense_variant | 0.17 |
gyrA | 9151 | p.Tyr617Cys | missense_variant | 0.15 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9603 | p.Val768Phe | missense_variant | 0.15 |
fgd1 | 491190 | c.408G>T | synonymous_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
fgd1 | 491774 | p.Arg331Met | missense_variant | 0.13 |
mshA | 576238 | c.891G>T | synonymous_variant | 0.13 |
mshA | 576380 | p.Leu345Val | missense_variant | 0.14 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 761053 | p.Pro416Leu | missense_variant | 0.17 |
rpoB | 761063 | c.1257C>A | synonymous_variant | 0.18 |
rpoB | 761332 | p.Pro509Leu | missense_variant | 0.14 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoB | 763098 | p.Glu1098* | stop_gained | 0.12 |
rpoC | 764669 | p.Pro434Thr | missense_variant | 0.33 |
rpoC | 765262 | c.1893C>A | synonymous_variant | 0.12 |
rpoC | 765421 | c.2052C>A | synonymous_variant | 0.12 |
rpoC | 766216 | c.2847T>C | synonymous_variant | 0.15 |
rpoC | 766467 | p.Glu1033Ala | missense_variant | 0.36 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775755 | p.Thr909Asn | missense_variant | 0.22 |
mmpL5 | 775952 | c.2529G>A | synonymous_variant | 0.22 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776749 | p.Phe578Leu | missense_variant | 0.2 |
mmpR5 | 778220 | c.-770G>A | upstream_gene_variant | 0.13 |
mmpL5 | 778938 | c.-459delC | upstream_gene_variant | 0.12 |
mmpR5 | 778996 | p.Val3Phe | missense_variant | 0.14 |
mmpL5 | 779211 | c.-731C>A | upstream_gene_variant | 0.12 |
rpsL | 781372 | c.-188T>G | upstream_gene_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1305020 | p.Ala697Asp | missense_variant | 0.13 |
Rv1258c | 1406135 | p.Glu402Asp | missense_variant | 0.13 |
Rv1258c | 1406917 | p.Ile142Val | missense_variant | 0.11 |
embR | 1416970 | c.378C>T | synonymous_variant | 0.13 |
embR | 1417001 | p.Val116Gly | missense_variant | 0.15 |
embR | 1417399 | c.-52G>A | upstream_gene_variant | 0.17 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1674152 | p.Pro238Arg | missense_variant | 0.5 |
inhA | 1674497 | p.Pro99Gln | missense_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101725 | p.Thr440Ala | missense_variant | 0.11 |
ndh | 2101967 | p.Arg359Leu | missense_variant | 0.11 |
ndh | 2102205 | p.Val280Phe | missense_variant | 0.22 |
ndh | 2102267 | p.Val259Ala | missense_variant | 0.18 |
ndh | 2103225 | c.-183A>C | upstream_gene_variant | 0.43 |
katG | 2154008 | p.Ser702Pro | missense_variant | 0.11 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155278 | c.834C>A | synonymous_variant | 0.2 |
katG | 2155529 | p.Glu195* | stop_gained | 0.12 |
katG | 2156256 | c.-145C>A | upstream_gene_variant | 0.14 |
katG | 2156499 | c.-388C>A | upstream_gene_variant | 0.15 |
katG | 2156543 | c.-432G>A | upstream_gene_variant | 0.22 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168437 | p.Leu726Ile | missense_variant | 0.11 |
PPE35 | 2168485 | p.Asn710Asp | missense_variant | 0.11 |
PPE35 | 2169138 | p.Thr492Met | missense_variant | 0.2 |
PPE35 | 2169574 | p.Phe347Leu | missense_variant | 0.11 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.14 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.15 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 1.0 |
Rv1979c | 2221838 | p.Gly443Cys | missense_variant | 0.12 |
Rv1979c | 2222951 | p.Val72Ile | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288879 | c.363G>T | synonymous_variant | 0.18 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
kasA | 2518251 | p.Leu46Pro | missense_variant | 0.12 |
eis | 2714255 | p.Tyr360His | missense_variant | 0.25 |
eis | 2714807 | p.Glu176* | stop_gained | 0.14 |
eis | 2715303 | p.Glu10Asp | missense_variant | 0.13 |
eis | 2715328 | p.Thr2Asn | missense_variant | 0.14 |
eis | 2715363 | c.-31G>C | upstream_gene_variant | 0.17 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.2 |
folC | 2746873 | p.Met242Ile | missense_variant | 0.14 |
folC | 2746981 | c.618T>C | synonymous_variant | 0.13 |
folC | 2747353 | c.246C>T | synonymous_variant | 0.12 |
folC | 2747447 | p.Ser51Ile | missense_variant | 0.18 |
folC | 2747652 | c.-54G>T | upstream_gene_variant | 0.15 |
folC | 2747777 | c.-179C>T | upstream_gene_variant | 0.2 |
pepQ | 2859349 | p.Gln357Arg | missense_variant | 0.18 |
ribD | 2986925 | c.87C>A | synonymous_variant | 0.11 |
ribD | 2987414 | c.576C>T | synonymous_variant | 0.11 |
Rv2752c | 3065265 | c.927C>G | synonymous_variant | 0.17 |
Rv2752c | 3065555 | c.636dupG | frameshift_variant | 0.17 |
thyX | 3067720 | p.Ala76Ser | missense_variant | 0.15 |
thyA | 3074306 | p.Ala56Ser | missense_variant | 0.19 |
thyA | 3074574 | c.-103G>A | upstream_gene_variant | 0.17 |
thyA | 3074645 | c.-174T>G | upstream_gene_variant | 0.27 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087228 | p.Ala137Ser | missense_variant | 0.17 |
Rv3083 | 3448883 | p.Glu127Val | missense_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474102 | c.96C>T | synonymous_variant | 0.2 |
fprA | 3474393 | c.387C>A | synonymous_variant | 0.17 |
fprA | 3475075 | p.Val357Ile | missense_variant | 0.15 |
Rv3236c | 3613243 | c.-127C>A | upstream_gene_variant | 0.12 |
fbiA | 3640381 | c.-162T>C | upstream_gene_variant | 0.62 |
fbiB | 3640863 | c.-672C>T | upstream_gene_variant | 0.33 |
fbiB | 3642023 | c.489C>G | synonymous_variant | 0.18 |
fbiB | 3642185 | c.651G>T | synonymous_variant | 0.2 |
fbiB | 3642768 | p.Leu412Met | missense_variant | 0.13 |
rpoA | 3877839 | c.669G>C | synonymous_variant | 0.17 |
rpoA | 3878074 | p.Gly145Ala | missense_variant | 0.4 |
rpoA | 3878079 | c.429C>A | synonymous_variant | 0.5 |
ddn | 3986960 | c.117C>G | synonymous_variant | 0.1 |
clpC1 | 4038186 | p.Ala840Glu | missense_variant | 0.4 |
clpC1 | 4039142 | p.Gln521His | missense_variant | 0.11 |
clpC1 | 4039535 | c.1170C>A | synonymous_variant | 0.13 |
clpC1 | 4040556 | p.Glu50Gly | missense_variant | 0.1 |
embC | 4240172 | p.Val104Met | missense_variant | 1.0 |
embC | 4240449 | p.Gln196Arg | missense_variant | 0.12 |
embC | 4241562 | p.Arg567His | missense_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embC | 4242461 | p.Gly867Cys | missense_variant | 0.25 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243323 | p.Val31Ile | missense_variant | 0.88 |
embA | 4244525 | c.1293G>A | synonymous_variant | 0.17 |
embA | 4244999 | c.1767G>T | synonymous_variant | 0.22 |
embB | 4246049 | c.-465G>T | upstream_gene_variant | 0.12 |
embB | 4246578 | p.Ser22Phe | missense_variant | 0.18 |
embB | 4247065 | p.Gln184His | missense_variant | 0.12 |
embB | 4247113 | c.600G>C | synonymous_variant | 0.15 |
embB | 4247865 | p.Ala451Glu | missense_variant | 0.13 |
embB | 4247876 | p.Leu455Met | missense_variant | 0.12 |
embB | 4248553 | c.2040C>T | synonymous_variant | 0.14 |
embB | 4249095 | p.Ala861Glu | missense_variant | 0.18 |
embB | 4249648 | c.3135G>A | synonymous_variant | 0.17 |
aftB | 4267195 | p.Pro548Thr | missense_variant | 0.12 |
aftB | 4268150 | p.Met229Ile | missense_variant | 0.17 |
ethA | 4326154 | c.1320G>T | synonymous_variant | 0.14 |
ethA | 4326376 | c.1098G>T | synonymous_variant | 0.14 |
ethR | 4326679 | c.-870C>A | upstream_gene_variant | 0.17 |
ethA | 4327002 | p.Val158Ile | missense_variant | 0.22 |
ethA | 4327344 | p.Thr44Ala | missense_variant | 0.14 |
ethR | 4327902 | p.Lys118Asn | missense_variant | 0.12 |
ethA | 4328377 | c.-904C>A | upstream_gene_variant | 0.12 |
whiB6 | 4338239 | p.Leu95Met | missense_variant | 0.13 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407831 | c.372G>T | synonymous_variant | 0.15 |
gid | 4408242 | c.-40T>C | upstream_gene_variant | 0.1 |