TB-Profiler result

Run: ERR1950062
Summary

Run ID: ERR1950062

Sample name:

Date: 31-03-2023 15:38:52

Number of reads: 692171

Percentage reads mapped: 99.15

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 8086 p.Asp262Gly missense_variant 0.14
gyrA 8274 p.Lys325* stop_gained 0.23
mshA 575381 c.34T>C synonymous_variant 0.21
mshA 575980 p.Asp211Glu missense_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 759789 c.-18G>T upstream_gene_variant 0.2
rpoB 760395 p.Lys197Glu missense_variant 0.15
rpoB 761163 p.Gly453Arg missense_variant 0.12
rpoC 764838 p.Val490Gly missense_variant 0.17
rpoC 766440 p.Ile1024Thr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775879 p.Thr868Ser missense_variant 0.33
mmpL5 778959 c.-479T>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303867 p.Asp313Tyr missense_variant 0.25
fbiC 1304123 p.Tyr398Ser missense_variant 0.14
fbiC 1304492 p.Asp521Ala missense_variant 0.29
Rv1258c 1406600 p.Phe247Leu missense_variant 0.25
Rv1258c 1406641 p.Thr234Pro missense_variant 0.22
embR 1416232 c.1116T>C synonymous_variant 0.14
embR 1416746 p.His201Pro missense_variant 0.38
atpE 1461265 p.Phe74Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473278 n.1433T>A non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474674 n.1017A>T non_coding_transcript_exon_variant 0.22
rrl 1476283 n.2626A>T non_coding_transcript_exon_variant 0.25
rrl 1476631 n.2974G>C non_coding_transcript_exon_variant 0.18
fabG1 1673570 p.Val44Gly missense_variant 0.2
inhA 1674356 p.Asp52Ala missense_variant 0.18
inhA 1674707 p.Glu169Val missense_variant 0.29
rpsA 1833618 p.Ile26Thr missense_variant 0.12
tlyA 1917788 c.-152A>G upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101821 p.Lys408Glu missense_variant 0.17
ndh 2102177 p.Leu289His missense_variant 0.18
ndh 2102631 p.Met138Leu missense_variant 0.3
katG 2154457 p.Ile552Lys missense_variant 0.2
katG 2155587 c.525G>T synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169777 p.Phe279Ser missense_variant 0.22
PPE35 2169903 p.Leu237Gln missense_variant 0.4
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170178 c.435T>G synonymous_variant 0.31
PPE35 2170458 p.Leu52Arg missense_variant 0.2
Rv1979c 2222830 p.Phe112Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289311 c.-70A>T upstream_gene_variant 0.25
pncA 2289785 c.-544A>G upstream_gene_variant 0.2
kasA 2518066 c.-49A>C upstream_gene_variant 0.33
kasA 2519285 p.Tyr391Asn missense_variant 0.33
ahpC 2725952 c.-241T>C upstream_gene_variant 0.22
folC 2747075 p.Val175Gly missense_variant 0.4
folC 2747701 c.-103T>A upstream_gene_variant 0.33
pepQ 2859416 c.1002delC frameshift_variant 0.25
ribD 2986800 c.-39T>A upstream_gene_variant 0.25
ribD 2986923 p.Pro29Thr missense_variant 0.27
ribD 2987023 p.Met62Arg missense_variant 0.29
ribD 2987396 c.558T>G synonymous_variant 0.14
Rv2752c 3064636 p.Val519Glu missense_variant 0.18
Rv2752c 3065080 p.His371Leu missense_variant 0.22
Rv2752c 3066313 c.-122T>G upstream_gene_variant 0.17
thyX 3067554 p.Ile131Asn missense_variant 0.5
thyX 3067870 p.Thr26Pro missense_variant 0.21
ald 3087925 p.Val369Gly missense_variant 0.17
Rv3083 3448450 c.-54A>G upstream_gene_variant 0.29
fprA 3474103 p.Asp33Asn missense_variant 0.22
Rv3236c 3612383 p.Phe245Ser missense_variant 0.3
Rv3236c 3612581 p.Leu179Arg missense_variant 0.2
Rv3236c 3613010 p.Tyr36Phe missense_variant 0.33
Rv3236c 3613146 c.-30T>G upstream_gene_variant 0.25
fbiA 3640546 p.Lys2Glu missense_variant 0.14
fbiB 3641668 p.Val45Gly missense_variant 0.43
fbiB 3642007 p.Asn158Thr missense_variant 0.33
fbiB 3642691 p.Val386Asp missense_variant 0.38
alr 3840588 p.Lys278Ile missense_variant 0.27
alr 3841299 p.Asp41Gly missense_variant 0.14
rpoA 3878467 p.Leu14His missense_variant 0.33
ddn 3986961 p.Thr40Ala missense_variant 0.18
ddn 3987299 c.456A>C stop_lost&splice_region_variant 0.24
clpC1 4038874 p.Thr611Pro missense_variant 0.2
clpC1 4039797 p.Asp303Ala missense_variant 0.29
embC 4240699 c.837C>A synonymous_variant 0.17
embC 4241657 p.Ser599Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242745 c.-488A>C upstream_gene_variant 0.2
embA 4245196 p.Ile655Asn missense_variant 0.33
embA 4246450 p.Val1073Ala missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4248036 p.Val508Gly missense_variant 0.14
embB 4249573 c.3060T>C synonymous_variant 0.15
aftB 4268826 p.Val4Gly missense_variant 0.4
aftB 4268832 p.Val2Gly missense_variant 0.33
ubiA 4269216 p.Ile206Met missense_variant 0.18
ethR 4327768 p.Thr74Pro missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407612 c.591T>G synonymous_variant 0.25
gid 4407893 p.Met104Val missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0