TB-Profiler result

Run: ERR1750944
Summary

Run ID: ERR1750944

Sample name:

Date: 31-03-2023 15:04:15

Number of reads: 2484639

Percentage reads mapped: 93.36

Strain: lineage4.1.2

Drug-resistance: Other

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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 1.0
lineage4.1.2 Euro-American T;H None 0.99
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
ethA 4326669 p.Gln269* stop_gained 0.5 ethionamide
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
gyrB 5299 c.60C>G synonymous_variant 0.11
gyrB 5742 p.Gly168Glu missense_variant 0.17
gyrB 5872 c.633G>A synonymous_variant 0.15
gyrA 6355 c.-947G>A upstream_gene_variant 0.2
gyrA 7300 c.-2A>T upstream_gene_variant 0.25
gyrA 7314 p.Thr5Ser missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7455 p.His52Tyr missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8134 c.835_837delAAC conservative_inframe_deletion 0.25
gyrA 8190 p.Ala297Ser missense_variant 0.22
gyrA 8822 c.1521C>T synonymous_variant 0.18
gyrA 8873 c.1572A>T synonymous_variant 0.17
gyrA 8879 c.1578C>A synonymous_variant 0.15
gyrA 9074 c.1773G>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491500 p.Glu240Lys missense_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491662 p.Val294Phe missense_variant 0.22
fgd1 491745 c.963G>T synonymous_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.37
rpoB 759856 p.Arg17Leu missense_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 0.88
rpoB 760490 c.684C>A synonymous_variant 0.22
rpoB 763255 p.Glu1150Val missense_variant 0.2
rpoC 763431 p.Arg21Lys missense_variant 0.22
rpoC 763444 p.Tyr25* stop_gained 0.2
rpoC 763524 p.Phe52Ser missense_variant 0.25
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14
rpoC 764410 c.1041G>C synonymous_variant 0.17
rpoC 764431 c.1062G>C synonymous_variant 0.17
rpoC 764434 c.1065A>G synonymous_variant 0.17
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.17
rpoC 764441 p.Ile358Leu missense_variant 0.2
rpoC 764446 c.1077T>C synonymous_variant 0.22
rpoC 764449 c.1080G>C synonymous_variant 0.2
rpoC 764452 c.1083T>C synonymous_variant 0.2
rpoC 764461 c.1092A>G synonymous_variant 0.2
rpoC 764485 c.1116G>C synonymous_variant 0.25
rpoC 764497 c.1128A>G synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.25
rpoC 764503 c.1134G>C synonymous_variant 0.29
rpoC 765113 p.Val582Leu missense_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765649 c.2280C>T synonymous_variant 0.18
rpoC 766297 c.2928G>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776154 p.Leu776* stop_gained 0.25
mmpL5 776197 p.Ala762Thr missense_variant 0.17
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 778077 p.Thr135Asn missense_variant 0.22
mmpL5 778091 p.Trp130* stop_gained 0.22
mmpL5 778540 c.-60G>T upstream_gene_variant 0.17
mmpL5 778594 c.-114C>T upstream_gene_variant 0.18
mmpS5 778673 p.Pro78Leu missense_variant 0.18
mmpS5 778679 p.Ala76Val missense_variant 0.2
mmpL5 778843 c.-363C>T upstream_gene_variant 0.5
mmpL5 778855 c.-375G>T upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800809 c.1A>G start_lost 0.14
rplC 800823 c.15C>G synonymous_variant 0.14
fbiC 1303395 p.Trp155Cys missense_variant 0.18
fbiC 1303641 c.711C>T synonymous_variant 0.18
embR 1417250 p.Pro33His missense_variant 0.5
atpE 1461276 p.Thr78Ser missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.36
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.27
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.27
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.21
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.21
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.15
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.12
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.18
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.12
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.13
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.13
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.13
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.27
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.15
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.27
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.27
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.13
rrs 1472694 n.849C>A non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472801 n.956G>A non_coding_transcript_exon_variant 0.18
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.25
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.38
rrs 1472841 n.996G>A non_coding_transcript_exon_variant 0.29
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.33
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.29
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.2
rrs 1472874 n.1029C>T non_coding_transcript_exon_variant 0.22
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.3
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.3
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.13
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.13
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.33
rrs 1472960 n.1115G>A non_coding_transcript_exon_variant 0.33
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.36
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.45
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.45
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.45
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.42
rrs 1472986 n.1141C>T non_coding_transcript_exon_variant 0.38
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.38
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.38
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.42
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.29
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.24
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.18
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.2
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.19
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.19
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrl 1474938 n.1281G>A non_coding_transcript_exon_variant 0.25
rrl 1474965 n.1308G>A non_coding_transcript_exon_variant 0.22
rrl 1475494 n.1837T>A non_coding_transcript_exon_variant 0.2
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.16
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.15
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.19
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.15
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.22
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.22
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476659 n.3002A>T non_coding_transcript_exon_variant 0.18
fabG1 1673284 c.-156G>A upstream_gene_variant 0.33
fabG1 1673777 p.Leu113His missense_variant 0.17
inhA 1674720 c.519G>A synonymous_variant 0.17
rpsA 1834361 c.820T>C synonymous_variant 0.29
rpsA 1834366 c.825A>G synonymous_variant 0.33
rpsA 1834369 c.828C>G synonymous_variant 0.33
rpsA 1834378 c.837T>G synonymous_variant 0.4
rpsA 1834384 c.843A>G synonymous_variant 0.33
rpsA 1834395 p.Arg285Gln missense_variant 0.29
rpsA 1834397 p.His286Val missense_variant 0.29
rpsA 1834411 c.870T>C synonymous_variant 0.43
rpsA 1834423 c.882G>T synonymous_variant 0.22
rpsA 1834427 p.Ile296Val missense_variant 0.2
rpsA 1834431 p.Val297Ala missense_variant 0.2
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.22
rpsA 1834456 c.915T>C synonymous_variant 0.22
rpsA 1834468 c.927A>G synonymous_variant 0.25
rpsA 1834482 p.Glu314Ala missense_variant 0.25
rpsA 1834486 p.Glu315Asp missense_variant 0.29
rpsA 1834489 c.948T>C synonymous_variant 0.43
rpsA 1834501 c.960G>C synonymous_variant 0.25
rpsA 1834945 c.1404C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101657 c.1386C>A synonymous_variant 0.25
ndh 2101681 c.1362C>A synonymous_variant 0.22
ndh 2102538 p.Lys169Gln missense_variant 0.4
ndh 2103018 p.Ala9Thr missense_variant 0.17
katG 2155942 p.Pro57Arg missense_variant 0.13
katG 2156447 c.-336C>A upstream_gene_variant 0.15
katG 2156538 c.-427A>G upstream_gene_variant 0.18
Rv1979c 2222230 p.Met312Lys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289775 c.-534C>T upstream_gene_variant 0.29
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714569 p.Ala255Gly missense_variant 0.23
ahpC 2726338 p.Val49Gly missense_variant 0.6
folC 2747573 p.Pro9Leu missense_variant 0.15
ribD 2987140 p.Val101Asp missense_variant 0.22
ribD 2987545 p.Thr236Asn missense_variant 0.17
Rv2752c 3064965 c.1227G>T synonymous_variant 0.14
Rv2752c 3065956 p.Leu79Ser missense_variant 0.86
thyX 3068114 c.-169G>T upstream_gene_variant 0.33
thyA 3073718 p.Asp252Asn missense_variant 0.22
thyA 3074022 c.437_449delGTCATGCGTTCTT frameshift_variant 0.29
thyA 3074645 c.-174T>G upstream_gene_variant 0.46
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448372 c.-132T>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474061 p.Ala19Thr missense_variant 0.22
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiB 3641706 p.Gly58Ser missense_variant 0.15
alr 3840709 p.Ser238Thr missense_variant 0.18
clpC1 4038790 c.1915C>T synonymous_variant 0.16
clpC1 4038795 p.Ser637Thr missense_variant 0.15
clpC1 4038810 p.Gln632Ser missense_variant 0.21
clpC1 4038812 c.1893T>C synonymous_variant 0.22
clpC1 4038815 c.1890G>T synonymous_variant 0.23
clpC1 4038860 c.1845G>C synonymous_variant 0.23
clpC1 4038878 c.1827A>G synonymous_variant 0.27
clpC1 4038890 c.1815G>A synonymous_variant 0.31
clpC1 4038911 c.1794G>T synonymous_variant 0.29
clpC1 4038917 c.1788C>T synonymous_variant 0.29
clpC1 4038923 c.1782A>G synonymous_variant 0.31
clpC1 4038926 c.1779G>T synonymous_variant 0.31
clpC1 4038941 c.1764G>C synonymous_variant 0.3
clpC1 4038944 c.1761C>T synonymous_variant 0.3
clpC1 4038953 c.1752A>G synonymous_variant 0.3
clpC1 4038956 c.1749T>C synonymous_variant 0.27
clpC1 4038965 c.1740T>C synonymous_variant 0.33
clpC1 4038971 c.1734T>C synonymous_variant 0.33
clpC1 4038974 c.1731T>C synonymous_variant 0.33
clpC1 4038980 c.1725C>T synonymous_variant 0.33
clpC1 4038986 p.Asp573Glu missense_variant 0.38
clpC1 4038989 c.1716T>C synonymous_variant 0.38
clpC1 4038997 c.1708T>C synonymous_variant 0.38
clpC1 4039004 c.1701C>G synonymous_variant 0.38
clpC1 4039019 c.1686G>C synonymous_variant 0.38
clpC1 4039022 c.1683A>G synonymous_variant 0.29
panD 4043873 p.Gly137Ser missense_variant 0.25
panD 4043878 c.403delC frameshift_variant 0.25
embC 4240836 p.Gly325Asp missense_variant 0.18
embC 4241872 c.2010G>A synonymous_variant 0.33
embC 4241956 c.2094A>T synonymous_variant 0.4
embC 4242011 p.Leu717Phe missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246294 p.Trp1021Leu missense_variant 0.2
embB 4247183 p.Gly224Arg missense_variant 0.14
embB 4249108 c.2595G>T synonymous_variant 0.17
embB 4249234 c.2721C>A synonymous_variant 0.14
aftB 4267286 p.His517Gln missense_variant 0.4
aftB 4267295 c.1542G>A synonymous_variant 0.4
aftB 4268931 c.-95C>T upstream_gene_variant 0.18
ethA 4326392 p.Val361Glu missense_variant 0.15
ethA 4326652 p.Glu274Asp missense_variant 0.4
ethA 4326656 p.Pro273Leu missense_variant 0.4
ethA 4327300 p.Asp58Glu missense_variant 0.33
ethR 4327402 c.-147C>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0