Run ID: SRR11972253
Sample name:
Date: 03-04-2023 05:33:38
Number of reads: 200545
Percentage reads mapped: 99.24
Strain: lineage1.1.3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.94 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 0.9 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.22 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.82 | isoniazid, ethionamide |
embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5436 | p.Asn66Ser | missense_variant | 0.6 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7717 | c.418delG | frameshift_variant | 0.67 |
gyrA | 7734 | p.Ile145Phe | missense_variant | 0.67 |
gyrA | 8105 | c.804G>A | synonymous_variant | 0.2 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.57 |
gyrA | 8650 | p.Arg450His | missense_variant | 0.4 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.3 |
rpoB | 760160 | c.354C>T | synonymous_variant | 0.4 |
rpoC | 762611 | c.-759C>T | upstream_gene_variant | 0.18 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763440 | p.Ser24Tyr | missense_variant | 0.2 |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
rpoC | 766616 | c.3247C>A | synonymous_variant | 0.14 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 778873 | c.-393G>A | upstream_gene_variant | 0.25 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.17 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781518 | c.-42G>A | upstream_gene_variant | 0.29 |
rpsL | 781884 | p.Asn109Asp | missense_variant | 0.14 |
fbiC | 1305123 | p.Asp731Glu | missense_variant | 0.18 |
Rv1258c | 1406782 | p.Ala187Ser | missense_variant | 0.33 |
Rv1258c | 1406867 | c.474G>A | synonymous_variant | 0.33 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.57 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474553 | n.896T>C | non_coding_transcript_exon_variant | 0.36 |
rrl | 1476618 | n.2961C>T | non_coding_transcript_exon_variant | 0.17 |
fabG1 | 1673215 | c.-225G>C | upstream_gene_variant | 0.64 |
ndh | 2102148 | p.Arg299Trp | missense_variant | 0.8 |
ndh | 2102621 | p.Ile141Asn | missense_variant | 0.4 |
katG | 2154061 | p.Ser684Ile | missense_variant | 0.22 |
katG | 2154099 | c.2013G>C | synonymous_variant | 0.25 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155009 | p.Phe368Tyr | missense_variant | 0.22 |
katG | 2156490 | c.-379G>A | upstream_gene_variant | 0.14 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.17 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
PPE35 | 2168883 | p.Gly577Asp | missense_variant | 0.25 |
PPE35 | 2169316 | p.Asn433Asp | missense_variant | 0.17 |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.56 |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.56 |
Rv1979c | 2221836 | c.1329T>C | synonymous_variant | 0.2 |
Rv1979c | 2222671 | p.Thr165Lys | missense_variant | 0.17 |
Rv1979c | 2223184 | c.-20T>C | upstream_gene_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290065 | c.-824G>A | upstream_gene_variant | 0.33 |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.79 |
kasA | 2519140 | c.1026G>C | synonymous_variant | 0.14 |
kasA | 2519143 | c.1029G>C | synonymous_variant | 0.15 |
kasA | 2519153 | p.Ile347Val | missense_variant | 0.2 |
kasA | 2519267 | p.Val385Ile | missense_variant | 1.0 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
folC | 2746429 | c.1170C>T | synonymous_variant | 0.33 |
pepQ | 2859324 | c.1095C>T | synonymous_variant | 0.15 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3065540 | p.Val218Leu | missense_variant | 1.0 |
thyX | 3067468 | p.Ala160Thr | missense_variant | 0.67 |
thyA | 3074341 | p.Leu44Pro | missense_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087148 | p.Ser110Phe | missense_variant | 0.25 |
Rv3083 | 3449379 | c.876G>A | synonymous_variant | 0.4 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fprA | 3475296 | c.1290G>A | synonymous_variant | 0.29 |
whiB7 | 3568597 | p.Trp28* | stop_gained | 0.2 |
fbiB | 3641951 | c.417G>A | synonymous_variant | 0.4 |
alr | 3840917 | c.504A>G | synonymous_variant | 0.2 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.22 |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.15 |
rpoA | 3877610 | p.Lys300Glu | missense_variant | 0.22 |
rpoA | 3878339 | p.Asp57Asn | missense_variant | 0.83 |
rpoA | 3878589 | c.-82A>C | upstream_gene_variant | 0.33 |
ddn | 3987194 | c.351G>A | synonymous_variant | 0.13 |
clpC1 | 4038778 | p.Glu643* | stop_gained | 0.33 |
clpC1 | 4039058 | p.Phe549Leu | missense_variant | 0.5 |
clpC1 | 4040144 | c.561G>C | synonymous_variant | 0.22 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
clpC1 | 4040763 | c.-59C>A | upstream_gene_variant | 0.13 |
panD | 4044285 | c.-4A>T | upstream_gene_variant | 0.25 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.89 |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
embC | 4241748 | p.Val629Glu | missense_variant | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
embA | 4244025 | p.His265Tyr | missense_variant | 0.17 |
embA | 4244061 | p.Leu277Ile | missense_variant | 0.12 |
embA | 4244628 | p.Ile466Leu | missense_variant | 0.22 |
embA | 4244857 | p.Ala542Val | missense_variant | 0.18 |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
embA | 4246137 | p.Arg969Trp | missense_variant | 0.22 |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
embB | 4249684 | p.Trp1057* | stop_gained | 0.13 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.83 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.44 |
ethA | 4326794 | p.Arg227His | missense_variant | 0.29 |
ethR | 4327306 | c.-243G>A | upstream_gene_variant | 0.33 |
whiB6 | 4338243 | c.278delG | frameshift_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407835 | p.Trp123* | stop_gained | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
gid | 4407973 | p.Val77Gly | missense_variant | 0.25 |