TB-Profiler result

Run: ERR3078008
Summary

Run ID: ERR3078008

Sample name:

Date: 01-04-2023 00:16:12

Number of reads: 872269

Percentage reads mapped: 4.86

Strain: lineage4.6.1

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 0.97
lineage4.6 Euro-American T;LAM None 0.97
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.93
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 761131 p.Gly442Glu missense_variant 0.23 rifampicin
ahpC 2726139 c.-54C>T upstream_gene_variant 0.82 isoniazid
katG 2147784 c.-5529_*6104del transcript_ablation 1.0 isoniazid
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 7539 p.Thr80Ala missense_variant 0.86
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761102 c.1296A>G synonymous_variant 0.12
rpoB 761126 c.1320G>T synonymous_variant 0.23
rpoB 761133 p.Leu443Ile missense_variant 0.23
rpoB 761150 c.1344A>C synonymous_variant 0.21
rpoB 761151 p.Leu449Val missense_variant 0.21
rpoB 761156 c.1350G>C synonymous_variant 0.21
rpoB 761159 c.1353G>A synonymous_variant 0.22
rpoB 761162 c.1356G>C synonymous_variant 0.21
rpoB 761165 c.1359G>C synonymous_variant 0.21
rpoB 761168 c.1362C>G synonymous_variant 0.21
rpoB 761178 p.Ser458Thr missense_variant 0.21
rpoB 761195 c.1389G>C synonymous_variant 0.28
rpoB 761196 p.Leu464Phe missense_variant 0.24
rpoB 761204 c.1398C>G synonymous_variant 0.25
rpoB 761207 c.1401C>T synonymous_variant 0.29
rpoB 761220 p.Ser472Thr missense_variant 0.25
rpoB 761234 c.1428G>T synonymous_variant 0.25
rpoB 761235 p.Met477Val missense_variant 0.25
rpoB 761252 c.1446C>T synonymous_variant 0.13
rpoB 761255 c.1449T>G synonymous_variant 0.14
rpoC 762860 c.-510G>C upstream_gene_variant 0.17
rpoC 762863 c.-507T>C upstream_gene_variant 0.33
rpoB 762878 p.Ile1024Met missense_variant 0.53
rpoB 762879 p.Met1025Leu missense_variant 0.51
rpoB 762888 p.His1028Asn missense_variant 0.51
rpoC 762899 c.-471G>C upstream_gene_variant 0.53
rpoB 762911 p.Ile1035Met missense_variant 0.53
rpoC 762917 c.-453C>G upstream_gene_variant 0.53
rpoC 762920 c.-450C>T upstream_gene_variant 0.53
rpoC 762929 c.-441G>T upstream_gene_variant 0.5
rpoB 762930 p.Pro1042Ser missense_variant 0.5
rpoC 762936 c.-434_-432delTCGinsAGC upstream_gene_variant 0.49
rpoB 762939 p.Met1045Leu missense_variant 0.49
rpoB 762942 p.Ile1046Val missense_variant 0.5
rpoC 762965 c.-405T>C upstream_gene_variant 0.56
rpoC 762983 c.-387C>T upstream_gene_variant 0.54
rpoC 762989 c.-381G>T upstream_gene_variant 0.55
rpoB 763005 p.Cys1067Val missense_variant 0.42
rpoB 763014 p.Met1070Leu missense_variant 0.29
rpoB 763017 p.Gln1071Glu missense_variant 0.25
rpoC 763025 c.-345C>T upstream_gene_variant 0.19
rpoC 763028 c.-342T>C upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.17
rpoC 763034 c.-336C>G upstream_gene_variant 0.14
rpoC 764902 c.1533C>G synonymous_variant 0.12
rpoC 764948 c.1579T>C synonymous_variant 0.14
rpoC 764953 c.1584G>C synonymous_variant 0.14
rpoC 764958 p.Glu530Ala missense_variant 0.14
rpoC 764968 c.1599T>C synonymous_variant 0.16
rpoC 766142 c.2773C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.28
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.25
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.24
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.24
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.43
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.41
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.36
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.37
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.39
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.31
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.61
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.62
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.62
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.74
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.8
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.77
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.73
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.7
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.56
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.55
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.55
rrs 1472839 n.994C>G non_coding_transcript_exon_variant 0.48
rrs 1472842 n.997G>A non_coding_transcript_exon_variant 0.21
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.8
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.95
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.94
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.94
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.94
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.94
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.95
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.95
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.95
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.95
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.94
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.95
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.94
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.94
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.94
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.94
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.93
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.93
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.9
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.84
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.81
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.81
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.79
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.78
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.21
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.14
rrl 1475517 n.1860C>T non_coding_transcript_exon_variant 0.26
rrl 1475518 n.1861A>G non_coding_transcript_exon_variant 0.3
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.22
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.14
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.15
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.15
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.14
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.19
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.19
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.2
rrl 1475576 n.1919C>A non_coding_transcript_exon_variant 0.2
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.32
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.38
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.28
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.28
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.42
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.93
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.94
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.94
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.95
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.95
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.95
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.95
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.95
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.95
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.95
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.94
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.94
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.95
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.95
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.93
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.93
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.92
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.91
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.74
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.59
rrl 1476565 n.2908G>A non_coding_transcript_exon_variant 0.14
rrl 1476566 n.2909A>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102116 c.927G>T synonymous_variant 0.96
katG 2155691 c.421T>C synonymous_variant 0.29
katG 2155695 c.417C>G synonymous_variant 0.29
katG 2155704 c.408C>G synonymous_variant 0.33
katG 2155716 c.396T>G synonymous_variant 0.29
katG 2155722 c.390G>C synonymous_variant 0.33
katG 2155728 c.384G>C synonymous_variant 0.33
katG 2155740 p.Gly124Gln missense_variant 0.33
katG 2155743 c.369G>C synonymous_variant 0.33
katG 2155782 c.330C>G synonymous_variant 0.33
katG 2155785 c.327T>C synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21
ahpC 2726507 c.315G>T synonymous_variant 0.85
thyX 3067814 c.132T>C synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039097 c.1608G>C synonymous_variant 0.13
clpC1 4039106 c.1599G>C synonymous_variant 0.12
clpC1 4039112 c.1593C>G synonymous_variant 0.14
clpC1 4039121 c.1584T>C synonymous_variant 0.14
clpC1 4039142 c.1563A>G synonymous_variant 0.14
clpC1 4039145 c.1560G>C synonymous_variant 0.15
clpC1 4039169 p.Glu512Asp missense_variant 0.18
clpC1 4039172 c.1533A>G synonymous_variant 0.19
clpC1 4039178 c.1527G>C synonymous_variant 0.2
clpC1 4039183 c.1522T>C synonymous_variant 0.19
clpC1 4039186 c.1519C>T synonymous_variant 0.18
clpC1 4039190 c.1515C>G synonymous_variant 0.2
clpC1 4039298 c.1407T>C synonymous_variant 0.12
clpC1 4039391 c.1314T>G synonymous_variant 0.17
clpC1 4039409 c.1296T>C synonymous_variant 0.23
clpC1 4039412 c.1293T>G synonymous_variant 0.2
clpC1 4039415 p.Glu430Asp missense_variant 0.19
clpC1 4039430 c.1275T>C synonymous_variant 0.19
clpC1 4039442 c.1263A>G synonymous_variant 0.19
clpC1 4039454 c.1251A>G synonymous_variant 0.14
clpC1 4039463 c.1242C>G synonymous_variant 0.12
clpC1 4039466 c.1239T>C synonymous_variant 0.12
embC 4241042 p.Asn394Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.13