Run ID: SRR3105742
Sample name:
Date: 04-04-2023 05:07:06
Number of reads: 1471274
Percentage reads mapped: 98.44
Strain: lineage3;lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.44 |
lineage2 | East-Asian | Beijing | RD105 | 0.55 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.61 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.57 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 0.38 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7570 | p.Ala90Val | missense_variant | 0.48 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.52 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.32 | rifampicin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.65 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.79 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.34 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.7 | isoniazid |
pncA | 2288850 | c.391dupG | frameshift_variant | 0.3 | pyrazinamide, pyrazinamide |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.43 | ethambutol |
embB | 4247429 | p.Met306Val | missense_variant | 0.47 | ethambutol |
embB | 4247723 | p.Pro404Ser | missense_variant | 0.61 | ethambutol |
ethA | 4326547 | c.926dupA | frameshift_variant | 0.5 | ethionamide |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.55 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.47 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.32 |
rpoB | 760321 | p.Gln172Arg | missense_variant | 0.4 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.42 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.95 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.53 |
mmpR5 | 779048 | p.Val20Ala | missense_variant | 0.42 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.71 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.75 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472512 | n.667A>G | non_coding_transcript_exon_variant | 0.23 |
inhA | 1674952 | p.Pro251Ala | missense_variant | 0.35 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.48 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155653 | p.Lys153Asn | missense_variant | 0.46 |
katG | 2155724 | p.Ala130Thr | missense_variant | 0.45 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.94 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.19 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.21 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.47 |
eis | 2715579 | c.-247G>C | upstream_gene_variant | 0.29 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.48 |
pepQ | 2860572 | c.-154G>A | upstream_gene_variant | 0.45 |
Rv2752c | 3065080 | p.His371Arg | missense_variant | 0.12 |
Rv2752c | 3066319 | c.-128T>C | upstream_gene_variant | 0.33 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.24 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.97 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474243 | c.237C>T | synonymous_variant | 0.43 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.63 |
clpC1 | 4039932 | p.Gly258Val | missense_variant | 0.26 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.38 |
embC | 4242476 | p.Pro872Ala | missense_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242822 | p.Val987Gly | missense_variant | 0.35 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.61 |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.5 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.48 |
aftB | 4269564 | c.-728G>A | upstream_gene_variant | 0.53 |
ethA | 4327132 | p.Asn114Lys | missense_variant | 0.36 |
whiB6 | 4338286 | c.235delG | frameshift_variant | 0.26 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.45 |
gid | 4408018 | p.Gly62Val | missense_variant | 0.57 |
gid | 4408168 | p.Phe12Cys | missense_variant | 0.4 |