Run ID: ERR036185
Sample name:
Date: 31-03-2023 08:28:25
Number of reads: 1334475
Percentage reads mapped: 93.97
Strain: lineage4.9;lineage4.3.4.2.1;lineage4.3.4.1;lineage3;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.14 |
lineage2 | East-Asian | Beijing | RD105 | 0.06 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.74 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.59 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.06 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.07 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.6 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.11 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 0.38 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.12 | rifampicin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.15 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.11 | isoniazid |
pncA | 2288820 | p.Gln141Pro | missense_variant | 0.28 | pyrazinamide |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.41 | ethambutol |
gid | 4407816 | c.386delG | frameshift_variant | 0.1 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.36 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.81 |
fgd1 | 491604 | c.822G>C | synonymous_variant | 0.17 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.21 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.2 |
rpoB | 759831 | p.Thr9Pro | missense_variant | 0.31 |
rpoB | 762249 | p.Leu815Val | missense_variant | 0.24 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.17 |
rpoB | 762714 | p.Val970Met | missense_variant | 0.18 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.62 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.27 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.54 |
rpoC | 767305 | p.Tyr1312* | stop_gained | 0.24 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.53 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.15 |
mmpR5 | 779371 | p.Ala128Pro | missense_variant | 0.33 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.14 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.12 |
atpE | 1461019 | c.-26C>A | upstream_gene_variant | 0.27 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1472378 | n.533G>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.22 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102540 | p.Ala168Gly | missense_variant | 0.36 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.34 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.24 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.14 |
PPE35 | 2169866 | c.747G>C | synonymous_variant | 0.37 |
PPE35 | 2170461 | p.Gly51Glu | missense_variant | 0.25 |
Rv1979c | 2223145 | p.Arg7Lys | missense_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289138 | p.Leu35Arg | missense_variant | 0.12 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.14 |
pncA | 2289448 | c.-207G>A | upstream_gene_variant | 0.15 |
eis | 2714225 | p.Ala370Pro | missense_variant | 0.25 |
eis | 2714366 | p.Val323Leu | missense_variant | 0.29 |
eis | 2715586 | c.-254G>C | upstream_gene_variant | 0.44 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.23 |
Rv2752c | 3064741 | p.Gly484Ala | missense_variant | 0.3 |
Rv2752c | 3065008 | p.Pro395Arg | missense_variant | 0.22 |
Rv2752c | 3067191 | c.-1000G>A | upstream_gene_variant | 0.33 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.56 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.96 |
fbiD | 3339153 | p.Leu12Phe | missense_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.85 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.42 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.18 |
fbiB | 3642734 | c.1200G>C | synonymous_variant | 0.25 |
alr | 3840268 | p.Thr385Pro | missense_variant | 0.3 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.4 |
rpoA | 3878238 | p.Asp90Glu | missense_variant | 0.33 |
ddn | 3987013 | p.Gly57Ala | missense_variant | 0.3 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.75 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.13 |
clpC1 | 4039293 | p.Gly471Asp | missense_variant | 0.11 |
clpC1 | 4039363 | p.Ala448Pro | missense_variant | 0.28 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.23 |
embC | 4241429 | p.Phe523Val | missense_variant | 0.45 |
embC | 4241539 | c.1677T>C | synonymous_variant | 0.25 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.17 |
embC | 4242425 | p.Arg855Gly | missense_variant | 0.27 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.21 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.94 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.47 |
embC | 4242827 | p.Leu989Val | missense_variant | 0.25 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.2 |
embB | 4248730 | c.2217C>T | synonymous_variant | 0.18 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.12 |
aftB | 4268812 | p.Ser9Ala | missense_variant | 0.5 |
ubiA | 4269529 | p.Ala102Gly | missense_variant | 0.13 |
ethA | 4327229 | p.Leu82Pro | missense_variant | 0.11 |
ethA | 4327672 | c.-199G>A | upstream_gene_variant | 0.56 |
ethA | 4328212 | c.-740delC | upstream_gene_variant | 0.24 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.22 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.69 |