Run ID: SRR7755705
Sample name:
Date: 04-04-2023 20:15:56
Number of reads: 3567219
Percentage reads mapped: 76.49
Strain: lineage4.2.1;lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.25 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.73 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.75 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.23 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.25 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.77 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.26 | streptomycin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.64 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.75 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288764 | p.Thr160Ala | missense_variant | 0.21 | pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.76 | kanamycin |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.25 | para-aminosalicylic_acid |
thyA | 3073808 | p.Arg222Gly | missense_variant | 0.48 | para-aminosalicylic_acid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.77 | ethambutol |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.67 | ethambutol |
embB | 4247431 | p.Met306Ile | missense_variant | 0.25 | ethambutol |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.3 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.78 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.18 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.2 |
ccsA | 619969 | p.Val27Ile | missense_variant | 0.67 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.35 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.24 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.75 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.26 |
rpoC | 766779 | p.Glu1137Gly | missense_variant | 0.21 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.45 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.26 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.29 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.23 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472108 | n.263C>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472129 | n.284G>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472135 | n.290C>G | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472153 | n.308G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472708 | n.863T>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476091 | n.2434T>C | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.45 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.24 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.21 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.22 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.29 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.61 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.72 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.35 |
fbiB | 3641810 | c.276G>C | synonymous_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.97 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.21 |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.67 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.16 |
ethA | 4326339 | p.Asn379Asp | missense_variant | 0.28 |
ethA | 4326632 | p.His281Pro | missense_variant | 0.77 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.66 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.17 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.22 |