Run ID: ERR2512512
Sample name:
Date: 31-03-2023 19:04:58
Number of reads: 621559
Percentage reads mapped: 99.61
Strain: lineage3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2154932 | p.Thr394Ala | missense_variant | 0.1 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6963 | p.Arg575His | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8566 | p.Ile422Asn | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491293 | p.Pro171Thr | missense_variant | 0.15 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
fgd1 | 491791 | c.1009T>C | stop_lost&splice_region_variant | 0.11 |
mshA | 576763 | p.Trp472* | stop_gained | 0.25 |
ccsA | 619733 | c.-158G>A | upstream_gene_variant | 0.67 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763205 | c.-165G>A | upstream_gene_variant | 1.0 |
rpoC | 765588 | p.Pro740Gln | missense_variant | 0.17 |
rpoC | 766256 | p.Arg963Cys | missense_variant | 0.12 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776181 | p.Asp767Ala | missense_variant | 1.0 |
mmpL5 | 778910 | c.-430G>T | upstream_gene_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303008 | p.Leu26Phe | missense_variant | 0.15 |
fbiC | 1303212 | c.282C>A | synonymous_variant | 0.11 |
fbiC | 1304132 | p.Ala401Val | missense_variant | 0.14 |
embR | 1416510 | p.Arg280Cys | missense_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1833759 | p.Asp73Val | missense_variant | 0.12 |
tlyA | 1917876 | c.-64C>A | upstream_gene_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155970 | p.Leu48Met | missense_variant | 0.1 |
katG | 2156523 | c.-412G>A | upstream_gene_variant | 0.11 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168884 | p.Gly577Ser | missense_variant | 0.14 |
PPE35 | 2169386 | c.1227C>A | synonymous_variant | 0.17 |
PPE35 | 2169394 | p.Ala407Ser | missense_variant | 0.12 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.33 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.33 |
PPE35 | 2170497 | p.Ala39Asp | missense_variant | 0.11 |
Rv1979c | 2222470 | p.Phe232Ser | missense_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
pncA | 2290040 | c.-799A>T | upstream_gene_variant | 0.12 |
kasA | 2519241 | p.Pro376Arg | missense_variant | 0.18 |
kasA | 2519326 | c.1212C>T | synonymous_variant | 0.15 |
eis | 2715355 | c.-23G>T | upstream_gene_variant | 0.12 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.23 |
ahpC | 2726405 | c.213C>A | synonymous_variant | 0.12 |
ahpC | 2726410 | p.Asp73Gly | missense_variant | 0.11 |
ribD | 2987103 | p.Arg89Cys | missense_variant | 0.12 |
Rv2752c | 3065514 | c.678C>T | synonymous_variant | 0.11 |
Rv2752c | 3065567 | p.Pro209Ala | missense_variant | 0.11 |
thyX | 3067386 | p.Gly187Asp | missense_variant | 0.13 |
thyX | 3067486 | p.Phe154Ile | missense_variant | 0.17 |
thyX | 3067504 | p.Ala148Thr | missense_variant | 0.18 |
thyA | 3073818 | c.654G>T | synonymous_variant | 0.11 |
thyA | 3074645 | c.-174T>G | upstream_gene_variant | 0.29 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449771 | p.Pro423Leu | missense_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474138 | c.132T>C | synonymous_variant | 0.12 |
fprA | 3474399 | p.Trp131Cys | missense_variant | 0.11 |
Rv3236c | 3612130 | c.987G>A | synonymous_variant | 0.17 |
Rv3236c | 3612375 | p.Gly248Ser | missense_variant | 0.25 |
Rv3236c | 3613143 | c.-27A>G | upstream_gene_variant | 0.12 |
alr | 3841052 | c.369G>A | synonymous_variant | 0.11 |
alr | 3841590 | c.-170G>A | upstream_gene_variant | 1.0 |
rpoA | 3878397 | c.111G>C | synonymous_variant | 0.11 |
clpC1 | 4038917 | c.1788C>T | synonymous_variant | 0.12 |
clpC1 | 4040138 | c.567G>T | synonymous_variant | 0.12 |
clpC1 | 4040411 | c.294T>G | synonymous_variant | 0.13 |
clpC1 | 4040841 | c.-137C>T | upstream_gene_variant | 0.15 |
embC | 4241155 | c.1293C>T | synonymous_variant | 0.11 |
embC | 4241303 | p.Thr481Pro | missense_variant | 0.11 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4244847 | p.Gly539Cys | missense_variant | 0.17 |
embA | 4244851 | p.Arg540Leu | missense_variant | 0.17 |
embA | 4245001 | p.Phe590Ser | missense_variant | 0.13 |
embA | 4245618 | p.Asp796Asn | missense_variant | 0.12 |
embA | 4246105 | p.Pro958Gln | missense_variant | 0.15 |
embA | 4246117 | p.Pro962Gln | missense_variant | 0.15 |
embA | 4246203 | p.Arg991* | stop_gained | 0.17 |
embB | 4247052 | p.Asn180Thr | missense_variant | 0.11 |
embB | 4249354 | c.2841G>A | synonymous_variant | 0.15 |
embB | 4249461 | p.Pro983Leu | missense_variant | 0.2 |
aftB | 4267577 | p.His420Gln | missense_variant | 0.18 |
aftB | 4268719 | p.Asn40Asp | missense_variant | 1.0 |
ethA | 4326366 | p.Lys370Gln | missense_variant | 0.15 |
ethA | 4326483 | p.Arg331Cys | missense_variant | 0.22 |
ethA | 4327016 | p.Gly153Asp | missense_variant | 0.2 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4408144 | p.Arg20Leu | missense_variant | 0.14 |