Run ID: SRR1166181
Sample name:
Date: 03-04-2023 01:22:28
Number of reads: 216313
Percentage reads mapped: 6.34
Strain: lineage4
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.67 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
pncA | 2288850 | c.390_391dupGG | frameshift_variant | 0.8 | pyrazinamide, pyrazinamide |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 1.0 |
fgd1 | 491395 | p.Glu205Lys | missense_variant | 0.25 |
rpoB | 761680 | p.Glu625Val | missense_variant | 0.5 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.46 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.46 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.71 |
rpoC | 762899 | c.-471G>C | upstream_gene_variant | 0.78 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.75 |
rpoC | 762917 | c.-453C>G | upstream_gene_variant | 0.75 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.75 |
rpoC | 762929 | c.-441G>T | upstream_gene_variant | 0.81 |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.81 |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.81 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.81 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.83 |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.87 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.83 |
rpoC | 762989 | c.-381G>T | upstream_gene_variant | 0.76 |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.69 |
rpoB | 763014 | p.Met1070Leu | missense_variant | 0.75 |
rpoB | 763017 | p.Gln1071Glu | missense_variant | 0.75 |
rpoC | 763025 | c.-345C>T | upstream_gene_variant | 0.75 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.75 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.75 |
rpoC | 763034 | c.-336C>G | upstream_gene_variant | 0.75 |
rpoC | 764230 | p.Gln287His | missense_variant | 0.33 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
rpoC | 764902 | c.1533C>G | synonymous_variant | 0.75 |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.75 |
rpoC | 764912 | p.Met515Val | missense_variant | 0.75 |
rpoC | 764918 | p.Val517Ile | missense_variant | 1.0 |
rpoC | 764932 | c.1563C>G | synonymous_variant | 1.0 |
rpoC | 764935 | c.1566T>C | synonymous_variant | 1.0 |
rpoC | 764948 | c.1579T>C | synonymous_variant | 1.0 |
rpoC | 764953 | c.1584G>C | synonymous_variant | 1.0 |
rpoC | 764958 | p.Glu530Ala | missense_variant | 1.0 |
rpoC | 764964 | p.Phe532Tyr | missense_variant | 1.0 |
rpoC | 764968 | c.1599T>C | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776661 | p.Leu607His | missense_variant | 0.67 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.7 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472328 | n.483G>C | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472349 | n.504A>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472374 | n.529T>A | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472415 | n.570T>G | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472427 | n.582T>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.89 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.97 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.96 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.87 |
rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.84 |
rrs | 1472839 | n.994C>G | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472842 | n.997G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.8 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.97 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.92 |
rrs | 1473097 | n.1252G>C | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473099 | n.1254T>A | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.4 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473139 | n.1294T>C | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473147 | n.1302G>C | non_coding_transcript_exon_variant | 0.83 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.85 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.86 |
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.86 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.86 |
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473193 | n.1348G>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473204 | n.1359C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473248 | n.1403G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473249 | n.1404T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1473869 | n.212C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474535 | n.878A>G | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475490 | n.1833C>A | non_coding_transcript_exon_variant | 0.78 |
rrl | 1475517 | n.1860C>T | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475518 | n.1861A>G | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.97 |
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.94 |
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.94 |
rrl | 1475576 | n.1919C>A | non_coding_transcript_exon_variant | 0.94 |
rrl | 1475596 | n.1939G>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1475791 | n.2134A>G | non_coding_transcript_exon_variant | 0.65 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.63 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.63 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.63 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.98 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.99 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476565 | n.2908G>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476566 | n.2909A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476585 | n.2928A>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476595 | n.2938C>A | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476602 | n.2945G>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476607 | n.2950C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476608 | n.2951C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476611 | n.2954T>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476614 | n.2957A>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476619 | n.2962C>T | non_coding_transcript_exon_variant | 0.5 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169121 | p.Val498Met | missense_variant | 0.29 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
Rv1979c | 2223144 | p.Arg7Ser | missense_variant | 0.29 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073947 | c.525G>C | synonymous_variant | 1.0 |
thyA | 3073953 | c.519T>C | synonymous_variant | 1.0 |
thyA | 3073956 | c.516G>C | synonymous_variant | 1.0 |
thyA | 3073959 | c.513T>C | synonymous_variant | 1.0 |
thyA | 3073962 | p.Leu170Ile | missense_variant | 1.0 |
thyA | 3073971 | c.499_501delAGCinsTCG | synonymous_variant | 1.0 |
thyA | 3073977 | c.495A>G | synonymous_variant | 1.0 |
thyA | 3073983 | c.489C>G | synonymous_variant | 1.0 |
thyA | 3073989 | c.483T>C | synonymous_variant | 1.0 |
thyA | 3073995 | c.477G>C | synonymous_variant | 1.0 |
thyA | 3073999 | p.Arg158Lys | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612369 | p.Thr250Ala | missense_variant | 0.67 |
clpC1 | 4040000 | p.His235Ala | missense_variant | 0.6 |
clpC1 | 4040006 | p.Ile233Met | missense_variant | 0.33 |
clpC1 | 4040010 | p.Ala232Arg | missense_variant | 0.67 |
clpC1 | 4040015 | c.690G>A | synonymous_variant | 0.5 |
clpC1 | 4040021 | c.684A>G | synonymous_variant | 0.71 |
clpC1 | 4040032 | p.Val225Ile | missense_variant | 0.83 |
clpC1 | 4040033 | c.672G>C | synonymous_variant | 0.71 |
clpC1 | 4040045 | c.660C>G | synonymous_variant | 0.29 |
clpC1 | 4040048 | c.657C>T | synonymous_variant | 0.43 |
clpC1 | 4040051 | c.654C>T | synonymous_variant | 0.29 |
clpC1 | 4040057 | c.648C>T | synonymous_variant | 0.29 |
clpC1 | 4040066 | c.639G>A | synonymous_variant | 0.29 |
clpC1 | 4040069 | c.636G>C | synonymous_variant | 0.29 |
embB | 4249533 | p.Ala1007Val | missense_variant | 0.67 |
embB | 4249594 | c.3081G>A | synonymous_variant | 1.0 |
ethA | 4326632 | p.His281Pro | missense_variant | 1.0 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |