TB-Profiler result

Run: SRR1166181
Summary

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

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
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
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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