Run ID: ERR5908173
Sample name:
Date: 02-04-2023 00:52:02
Number of reads: 772508
Percentage reads mapped: 99.67
Strain: lineage4.3.3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6749 | p.Ala504Thr | missense_variant | 0.13 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
katG | 2155030 | p.Ala361Asp | missense_variant | 0.14 | isoniazid |
ethA | 4326880 | c.593delG | frameshift_variant | 0.11 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6634 | c.-668T>C | upstream_gene_variant | 0.11 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7562 | c.261C>T | synonymous_variant | 0.13 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 8435 | c.1134C>T | synonymous_variant | 0.12 |
gyrA | 8527 | p.Arg409Leu | missense_variant | 0.12 |
gyrA | 9046 | p.Tyr582Phe | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 490782 | c.-1G>C | upstream_gene_variant | 0.11 |
mshA | 575282 | c.-66C>T | upstream_gene_variant | 0.2 |
mshA | 575514 | p.Pro56Leu | missense_variant | 0.15 |
mshA | 576483 | p.Val379Ala | missense_variant | 0.29 |
ccsA | 620253 | c.363G>A | synonymous_variant | 0.15 |
rpoB | 759824 | p.Gln6His | missense_variant | 0.12 |
rpoB | 760508 | c.702G>T | synonymous_variant | 0.13 |
rpoB | 761720 | c.1914C>G | synonymous_variant | 0.22 |
rpoB | 761993 | c.2187C>T | synonymous_variant | 0.12 |
rpoB | 762178 | p.Arg791His | missense_variant | 0.17 |
rpoB | 763057 | p.Thr1084Ile | missense_variant | 0.13 |
rpoC | 763510 | c.141C>T | synonymous_variant | 0.11 |
rpoC | 764410 | c.1041G>T | synonymous_variant | 0.13 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 766096 | c.2727G>T | synonymous_variant | 0.22 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776887 | p.Asn532Asp | missense_variant | 0.11 |
mmpL5 | 777389 | p.Phe364Leu | missense_variant | 0.13 |
mmpL5 | 778663 | c.-183C>T | upstream_gene_variant | 0.15 |
mmpS5 | 778902 | p.Ile2Val | missense_variant | 0.1 |
mmpL5 | 778960 | c.-480G>A | upstream_gene_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800720 | c.-88delC | upstream_gene_variant | 0.11 |
fbiC | 1303930 | p.Pro334Thr | missense_variant | 0.11 |
fbiC | 1304716 | p.Ala596Ser | missense_variant | 0.2 |
fbiC | 1305202 | p.Arg758Gly | missense_variant | 0.1 |
Rv1258c | 1406276 | c.1065G>A | synonymous_variant | 0.13 |
Rv1258c | 1406299 | p.Val348Leu | missense_variant | 0.15 |
Rv1258c | 1406643 | p.Leu233Pro | missense_variant | 0.12 |
embR | 1416480 | p.Ala290Thr | missense_variant | 0.15 |
atpE | 1460985 | c.-59delA | upstream_gene_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471689 | n.-157T>C | upstream_gene_variant | 0.17 |
rrs | 1472019 | n.174G>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472975 | n.1130T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473312 | n.1467G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476225 | n.2568T>C | non_coding_transcript_exon_variant | 1.0 |
inhA | 1674276 | p.Ile25Met | missense_variant | 0.12 |
inhA | 1674874 | p.Arg225Ser | missense_variant | 0.11 |
rpsA | 1833438 | c.-104C>G | upstream_gene_variant | 0.14 |
rpsA | 1833726 | p.Val62Ala | missense_variant | 0.12 |
rpsA | 1834448 | p.Lys303Glu | missense_variant | 0.15 |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.94 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102058 | p.Val329Met | missense_variant | 0.13 |
ndh | 2102080 | c.963C>T | synonymous_variant | 0.13 |
ndh | 2102092 | c.951G>T | synonymous_variant | 0.14 |
ndh | 2102119 | c.924C>T | synonymous_variant | 0.14 |
ndh | 2102499 | p.Gly182Arg | missense_variant | 0.2 |
katG | 2154536 | p.Glu526Lys | missense_variant | 0.11 |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 1.0 |
katG | 2156418 | c.-307G>T | upstream_gene_variant | 0.22 |
PPE35 | 2168342 | c.2271T>A | synonymous_variant | 0.2 |
PPE35 | 2169253 | p.Ala454Ser | missense_variant | 0.29 |
PPE35 | 2169522 | p.Ala364Glu | missense_variant | 0.18 |
PPE35 | 2169692 | c.921C>A | synonymous_variant | 0.12 |
PPE35 | 2169750 | p.Gly288Val | missense_variant | 0.12 |
PPE35 | 2170292 | c.321G>A | synonymous_variant | 0.13 |
PPE35 | 2170445 | c.168G>T | synonymous_variant | 0.15 |
PPE35 | 2170498 | p.Ala39Ser | missense_variant | 0.17 |
Rv1979c | 2221962 | c.1203A>T | synonymous_variant | 0.12 |
Rv1979c | 2222778 | c.387C>T | synonymous_variant | 0.13 |
Rv1979c | 2222991 | c.174G>T | synonymous_variant | 0.13 |
Rv1979c | 2223156 | p.Gly3Arg | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288719 | p.Met175Leu | missense_variant | 0.11 |
pncA | 2288725 | p.Glu173Lys | missense_variant | 0.11 |
pncA | 2289951 | c.-710G>T | upstream_gene_variant | 0.21 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
eis | 2714376 | c.957G>T | synonymous_variant | 0.22 |
eis | 2714858 | p.Gly159Cys | missense_variant | 0.2 |
ahpC | 2726281 | p.Gln30Arg | missense_variant | 0.2 |
ahpC | 2726536 | p.Lys115Arg | missense_variant | 0.15 |
folC | 2746340 | p.Ala420Val | missense_variant | 1.0 |
folC | 2747194 | p.Asp135Glu | missense_variant | 0.11 |
folC | 2747292 | p.Ser103Thr | missense_variant | 0.18 |
folC | 2747727 | c.-129C>A | upstream_gene_variant | 0.11 |
pepQ | 2860254 | c.165C>A | synonymous_variant | 0.14 |
ribD | 2987158 | p.Gln107Arg | missense_variant | 0.25 |
Rv2752c | 3066110 | p.Gly28Cys | missense_variant | 0.17 |
thyX | 3067210 | c.736T>C | synonymous_variant | 0.11 |
thyX | 3067312 | p.Ala212Thr | missense_variant | 0.13 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086796 | c.-24C>A | upstream_gene_variant | 0.13 |
ald | 3087424 | p.Asp202Val | missense_variant | 0.11 |
ald | 3087444 | p.Ala209Ser | missense_variant | 0.12 |
fbiD | 3339087 | c.-31C>A | upstream_gene_variant | 0.17 |
fbiD | 3339135 | p.Asp6Glu | missense_variant | 0.18 |
fbiD | 3339263 | p.Ala49Val | missense_variant | 0.13 |
fbiD | 3339308 | p.Pro64Leu | missense_variant | 0.12 |
Rv3083 | 3448514 | p.His4Arg | missense_variant | 0.11 |
Rv3083 | 3448586 | p.Pro28His | missense_variant | 0.12 |
Rv3083 | 3449946 | c.1443C>T | synonymous_variant | 0.11 |
fprA | 3473946 | c.-61T>C | upstream_gene_variant | 0.15 |
fprA | 3473960 | c.-47T>C | upstream_gene_variant | 0.13 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475207 | p.Asp401Tyr | missense_variant | 0.12 |
Rv3236c | 3613201 | c.-85C>T | upstream_gene_variant | 0.12 |
fbiA | 3640424 | c.-118delT | upstream_gene_variant | 0.12 |
fbiB | 3642194 | p.Phe220Leu | missense_variant | 0.18 |
alr | 3840431 | c.990C>A | synonymous_variant | 0.12 |
alr | 3840882 | p.Arg180Leu | missense_variant | 0.2 |
alr | 3841014 | p.Arg136Pro | missense_variant | 0.11 |
rpoA | 3878495 | p.Gln5* | stop_gained | 0.2 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4039804 | p.Ala301Ser | missense_variant | 0.14 |
clpC1 | 4040587 | p.Glu40* | stop_gained | 0.22 |
embC | 4239950 | c.88C>A | synonymous_variant | 0.12 |
embC | 4240324 | c.462G>T | synonymous_variant | 0.13 |
embC | 4240546 | c.684G>T | synonymous_variant | 0.13 |
embC | 4241198 | p.Ile446Val | missense_variant | 0.12 |
embC | 4241650 | p.Leu596Phe | missense_variant | 0.13 |
embC | 4242323 | p.Gly821Ser | missense_variant | 0.33 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243099 | c.-134G>A | upstream_gene_variant | 0.22 |
embA | 4243853 | p.Met207Ile | missense_variant | 0.33 |
embA | 4244116 | p.Arg295Gln | missense_variant | 0.17 |
embA | 4244166 | p.Ala312Thr | missense_variant | 0.14 |
embA | 4244874 | p.Pro548Ser | missense_variant | 0.67 |
embB | 4247022 | p.Ala170Gly | missense_variant | 0.25 |
embB | 4247976 | p.Val488Asp | missense_variant | 0.1 |
embB | 4249364 | p.Glu951* | stop_gained | 0.13 |
aftB | 4267688 | c.1149G>A | synonymous_variant | 0.13 |
aftB | 4268198 | c.639C>A | synonymous_variant | 0.12 |
ethA | 4326242 | p.Asp411Gly | missense_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407851 | p.Arg118Cys | missense_variant | 0.12 |
gid | 4408000 | p.Ile68Asn | missense_variant | 0.12 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
gid | 4408254 | c.-52G>T | upstream_gene_variant | 0.15 |