Run ID: ERR2510765
Sample name:
Date: 31-03-2023 18:55:40
Number of reads: 613423
Percentage reads mapped: 96.87
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6735 | p.Asn499Thr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 1.0 | streptomycin |
rrs | 1472644 | n.799C>T | non_coding_transcript_exon_variant | 0.19 | streptomycin |
katG | 2154352 | p.Leu587Pro | missense_variant | 0.12 | isoniazid |
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289038 | p.Trp68* | stop_gained | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
embB | 4247729 | p.Gly406Cys | missense_variant | 1.0 | ethambutol |
ethA | 4326969 | c.504delC | frameshift_variant | 1.0 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7670 | c.369A>T | synonymous_variant | 0.1 |
gyrA | 8816 | c.1515C>T | synonymous_variant | 0.12 |
fgd1 | 490684 | c.-99G>A | upstream_gene_variant | 0.17 |
fgd1 | 491077 | p.Asn99Tyr | missense_variant | 0.17 |
mshA | 575965 | c.618C>T | synonymous_variant | 0.12 |
ccsA | 620843 | p.His318Leu | missense_variant | 0.11 |
rpoB | 759955 | p.Val50Gly | missense_variant | 1.0 |
rpoC | 764487 | p.Met373Thr | missense_variant | 0.11 |
rpoC | 765713 | p.Thr782Ala | missense_variant | 1.0 |
rpoC | 766691 | p.Gly1108Arg | missense_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777602 | p.Gln293His | missense_variant | 0.12 |
mmpL5 | 779298 | c.-818G>A | upstream_gene_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304443 | p.Ala505Ser | missense_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472113 | n.268T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472597 | n.752G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472842 | n.997G>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.3 |
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475729 | n.2072C>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.25 |
inhA | 1674855 | c.654C>T | synonymous_variant | 0.15 |
rpsA | 1834737 | p.Glu399Gly | missense_variant | 0.1 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154513 | c.1599G>T | synonymous_variant | 0.12 |
katG | 2155635 | c.477C>T | synonymous_variant | 0.11 |
katG | 2156420 | c.-309A>G | upstream_gene_variant | 0.11 |
PPE35 | 2168228 | c.2385C>T | synonymous_variant | 0.12 |
PPE35 | 2170636 | c.-24G>A | upstream_gene_variant | 0.1 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289698 | c.-458delT | upstream_gene_variant | 0.11 |
kasA | 2519184 | p.Leu357Pro | missense_variant | 0.14 |
kasA | 2519208 | p.Gly365Asp | missense_variant | 0.14 |
folC | 2746468 | c.1131G>T | synonymous_variant | 0.17 |
Rv2752c | 3064976 | p.Asn406Asp | missense_variant | 0.17 |
ald | 3087130 | p.Thr104Asn | missense_variant | 0.11 |
ald | 3087251 | c.434dupG | frameshift_variant | 1.0 |
fbiD | 3339178 | p.Ala21Ser | missense_variant | 0.11 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
Rv3236c | 3612084 | p.Gly345Ser | missense_variant | 0.11 |
fbiA | 3640901 | p.Gln120Arg | missense_variant | 1.0 |
fbiB | 3642178 | p.Ala215Val | missense_variant | 0.2 |
ddn | 3986904 | p.Met21Val | missense_variant | 0.11 |
clpC1 | 4038967 | p.Ile580Phe | missense_variant | 0.1 |
clpC1 | 4040129 | c.576C>T | synonymous_variant | 0.15 |
embC | 4239711 | c.-152C>A | upstream_gene_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4246006 | p.Leu925Pro | missense_variant | 0.11 |
embA | 4246057 | p.Val942Asp | missense_variant | 0.12 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.2 |
embB | 4246941 | p.Pro143Arg | missense_variant | 0.13 |
embB | 4247015 | p.Ser168Pro | missense_variant | 0.11 |
ubiA | 4269578 | c.255delC | frameshift_variant | 0.12 |
ubiA | 4269715 | p.Leu40Ser | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |