TB-Profiler result

Run: ERR2027233
Summary

Run ID: ERR2027233

Sample name:

Date: 31-03-2023 15:40:34

Number of reads: 2807790

Percentage reads mapped: 56.34

Strain: lineage4.1.2.1

Drug-resistance: RR-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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761085 p.Thr427Ser missense_variant 0.5 rifampicin
rpoB 761131 p.Gly442Glu missense_variant 0.5 rifampicin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576597 p.Met417Lys missense_variant 0.33
mshA 576701 p.Arg452Ser missense_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.5
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.5
rpoB 761102 c.1296A>G synonymous_variant 0.5
rpoB 761133 p.Leu443Val missense_variant 0.5
rpoB 762173 c.2367G>A synonymous_variant 0.18
rpoB 762176 c.2370T>G synonymous_variant 0.23
rpoB 762181 p.Asp792Ala missense_variant 0.25
rpoB 762185 c.2379G>C synonymous_variant 0.24
rpoB 762218 c.2412T>C synonymous_variant 0.35
rpoB 762221 c.2415G>A synonymous_variant 0.35
rpoB 762223 p.Thr806Ser missense_variant 0.32
rpoB 762225 p.Glu807Gln missense_variant 0.32
rpoB 762233 c.2427G>C synonymous_variant 0.29
rpoB 762239 c.2433G>A synonymous_variant 0.29
rpoB 762243 p.Arg813Lys missense_variant 0.3
rpoB 762254 c.2448T>C synonymous_variant 0.23
rpoB 762257 c.2451C>G synonymous_variant 0.22
rpoB 762266 c.2460T>C synonymous_variant 0.21
rpoB 762888 p.His1028Asn missense_variant 0.14
rpoC 762899 c.-471G>C upstream_gene_variant 0.17
rpoB 762911 p.Ile1035Met missense_variant 0.33
rpoC 762920 c.-450C>T upstream_gene_variant 0.38
rpoC 762923 c.-447C>G upstream_gene_variant 0.39
rpoC 762929 c.-441G>T upstream_gene_variant 0.39
rpoB 762939 p.Met1045Leu missense_variant 0.4
rpoB 762942 p.Ile1046Val missense_variant 0.4
rpoC 762965 c.-405T>C upstream_gene_variant 0.42
rpoC 762980 c.-390T>C upstream_gene_variant 0.28
rpoC 762989 c.-381G>C upstream_gene_variant 0.17
rpoC 764557 p.Asn396Lys missense_variant 0.62
rpoC 764560 c.1191T>C synonymous_variant 0.81
rpoC 764566 c.1197C>G synonymous_variant 0.9
rpoC 764575 c.1206T>G synonymous_variant 0.92
rpoC 764576 p.Ser403Ala missense_variant 0.92
rpoC 764582 p.Leu405Met missense_variant 0.93
rpoC 764585 p.Leu406Ile missense_variant 0.93
rpoC 764605 c.1236G>C synonymous_variant 0.94
rpoC 764611 c.1242G>C synonymous_variant 0.93
rpoC 764632 c.1263T>C synonymous_variant 0.91
rpoC 764650 c.1281G>T synonymous_variant 0.91
rpoC 764672 p.Gln435Tyr missense_variant 0.85
rpoC 764677 c.1308C>G synonymous_variant 0.84
rpoC 764678 p.Lys437Arg missense_variant 0.84
rpoC 764695 c.1326T>C synonymous_variant 0.81
rpoC 764701 c.1332C>G synonymous_variant 0.82
rpoC 764705 p.Leu446Lys missense_variant 0.81
rpoC 764716 c.1347G>T synonymous_variant 0.8
rpoC 764737 c.1368G>C synonymous_variant 0.26
rpoC 764844 p.Ala492Gly missense_variant 0.28
rpoC 764851 c.1482C>T synonymous_variant 0.57
rpoC 764858 p.Leu497Met missense_variant 0.68
rpoC 764869 c.1500C>T synonymous_variant 0.68
rpoC 764872 c.1503A>G synonymous_variant 0.68
rpoC 764875 c.1506C>G synonymous_variant 0.67
rpoC 764887 c.1518G>C synonymous_variant 0.65
rpoC 764888 c.1519T>C synonymous_variant 0.64
rpoC 764893 c.1524T>C synonymous_variant 0.65
rpoC 764902 c.1533C>G synonymous_variant 0.66
rpoC 764911 c.1542A>G synonymous_variant 0.7
rpoC 764912 p.Met515Val missense_variant 0.7
rpoC 764918 p.Val517Ile missense_variant 0.7
rpoC 764923 c.1554A>G synonymous_variant 0.7
rpoC 764935 c.1566T>C synonymous_variant 0.67
rpoC 764941 c.1572G>A synonymous_variant 0.7
rpoC 764948 c.1579T>C synonymous_variant 0.73
rpoC 764953 c.1584G>C synonymous_variant 0.75
rpoC 764956 c.1587T>C synonymous_variant 0.76
rpoC 764957 p.Glu530Thr missense_variant 0.76
rpoC 764968 c.1599T>C synonymous_variant 0.75
rpoC 764998 c.1629G>C synonymous_variant 0.48
rpoC 765002 p.Leu545Val missense_variant 0.32
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777352 p.Arg377Trp missense_variant 0.2
mmpL5 777362 p.Met373Ile missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781832 c.273T>G synonymous_variant 0.13
fbiC 1304076 c.1146C>T synonymous_variant 0.5
embR 1417109 p.Arg80His missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.28
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.69
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.79
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.81
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.85
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.84
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.82
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.82
rrs 1472243 n.398G>A non_coding_transcript_exon_variant 0.82
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.76
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.76
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.77
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.48
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.19
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.31
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.49
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.52
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.59
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.55
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.49
rrs 1472390 n.545T>C non_coding_transcript_exon_variant 0.48
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.47
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.23
rrs 1472414 n.569C>T non_coding_transcript_exon_variant 0.19
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.29
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.31
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.49
rrs 1472648 n.803G>C non_coding_transcript_exon_variant 0.41
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.26
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.51
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.85
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.89
rrs 1472716 n.871C>G non_coding_transcript_exon_variant 0.91
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.94
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.95
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.96
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.95
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.94
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.76
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.72
rrs 1472837 n.992C>T non_coding_transcript_exon_variant 0.29
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.52
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.91
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.98
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.98
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.98
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.99
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.99
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.99
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.99
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.99
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.99
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.99
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.99
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.99
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.99
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.99
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.98
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.98
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.97
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.97
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.95
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.94
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.67
rrs 1473084 n.1239T>G non_coding_transcript_exon_variant 0.19
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.26
rrs 1473131 n.1286G>A non_coding_transcript_exon_variant 0.38
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.83
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.87
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.87
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.9
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.91
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.92
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.91
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.91
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.34
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.2
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.25
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.8
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.81
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.84
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.84
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.33
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.9
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.92
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.93
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.94
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.93
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.95
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.94
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 0.94
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>T non_coding_transcript_exon_variant 0.97
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.97
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.93
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.93
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 0.93
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.94
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.94
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.27
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.69
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170226 c.386delA frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2859897 c.522C>A synonymous_variant 0.12
thyX 3067317 p.Arg210Leu missense_variant 0.13
thyX 3067655 c.291G>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612029 p.Ala363Val missense_variant 0.13
clpC1 4038773 c.1932T>C synonymous_variant 0.22
clpC1 4038776 p.Glu643Asp missense_variant 0.24
clpC1 4038781 p.Leu642Phe missense_variant 0.26
clpC1 4038795 p.Ser637Ile missense_variant 0.26
clpC1 4038805 p.Ile634Val missense_variant 0.27
clpC1 4038806 p.Glu633Asp missense_variant 0.27
clpC1 4038809 p.Gln632Pro missense_variant 0.27
clpC1 4038812 c.1893T>C synonymous_variant 0.27
clpC1 4038835 p.Phe624Leu missense_variant 0.35
clpC1 4038841 p.Val622Leu missense_variant 0.33
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 0.35
clpC1 4038849 p.Phe619Tyr missense_variant 0.35
clpC1 4038851 c.1854G>C synonymous_variant 0.36
clpC1 4038860 c.1845G>T synonymous_variant 0.34
clpC1 4038878 c.1827A>G synonymous_variant 0.33
clpC1 4038890 p.Glu605Asp missense_variant 0.18
clpC1 4039674 p.Pro344Lys missense_variant 0.16
clpC1 4039697 c.1008C>T synonymous_variant 0.62
clpC1 4039730 c.975C>G synonymous_variant 0.52
clpC1 4039739 c.966C>G synonymous_variant 0.34
clpC1 4039742 c.963C>T synonymous_variant 0.22
clpC1 4040021 c.684A>G synonymous_variant 0.2
clpC1 4040032 p.Val225Ile missense_variant 0.37
clpC1 4040033 c.672G>C synonymous_variant 0.27
clpC1 4040045 c.660C>G synonymous_variant 0.19
clpC1 4040054 c.651G>A synonymous_variant 0.38
embC 4241562 p.Arg567His missense_variant 0.15
embC 4241578 c.1716G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245645 p.Ala805Ser missense_variant 0.2
embB 4245854 c.-660C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0