TB-Profiler result

Run: ERR1949964
Summary

Run ID: ERR1949964

Sample name:

Date: 31-03-2023 15:35:54

Number of reads: 629688

Percentage reads mapped: 99.27

Strain: lineage4.8

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
lineage4.8 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
ethA 4327347 p.Gly43Cys missense_variant 0.2 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 5577 p.Ala113Val missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490882 p.Ser34Arg missense_variant 0.29
fgd1 491010 c.228C>A synonymous_variant 0.4
fgd1 491167 p.Phe129Val missense_variant 0.5
fgd1 491184 p.Glu134Asp missense_variant 0.25
mshA 575311 c.-37A>C upstream_gene_variant 0.27
mshA 575944 c.597T>G synonymous_variant 0.22
ccsA 619707 c.-184T>G upstream_gene_variant 0.29
ccsA 620312 p.Leu141Gln missense_variant 0.18
ccsA 620336 p.Leu149Arg missense_variant 0.17
rpoC 763353 c.-17A>T upstream_gene_variant 0.29
rpoC 766965 p.Glu1199Ala missense_variant 0.38
rpoC 767216 p.Tyr1283Asp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777590 c.891G>A synonymous_variant 1.0
mmpL5 777924 p.Val186Gly missense_variant 0.33
mmpS5 779658 c.-753T>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781615 p.Val19Gly missense_variant 0.2
rplC 801169 p.Lys121* stop_gained 0.25
rplC 801210 c.402T>G synonymous_variant 0.13
fbiC 1303086 c.156T>G synonymous_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304096 p.Val389Gly missense_variant 0.33
fbiC 1304458 p.Thr510Ser missense_variant 0.27
embR 1416222 p.Phe376Leu missense_variant 0.17
embR 1416232 p.Cys372Gly missense_variant 0.17
embR 1416543 p.Thr269Pro missense_variant 0.2
embR 1416635 p.Asp238Ala missense_variant 0.18
atpE 1460931 c.-114A>T upstream_gene_variant 0.22
atpE 1460948 c.-97A>T upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472335 n.490A>C non_coding_transcript_exon_variant 0.25
rrs 1472387 n.542T>G non_coding_transcript_exon_variant 0.3
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475812 n.2155T>A non_coding_transcript_exon_variant 0.25
rrl 1476012 n.2355T>A non_coding_transcript_exon_variant 0.4
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
rpsA 1833720 p.Glu60Ala missense_variant 0.27
rpsA 1834969 p.Lys476Asn missense_variant 0.4
tlyA 1917872 c.-68T>G upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101721 p.Arg441Gln missense_variant 0.33
ndh 2102450 p.Lys198Met missense_variant 0.18
ndh 2102609 p.Leu145* stop_gained 0.25
katG 2154231 c.1881G>T synonymous_variant 0.17
katG 2156319 c.-208A>T upstream_gene_variant 0.25
katG 2156453 c.-342C>A upstream_gene_variant 0.22
katG 2156458 c.-347T>G upstream_gene_variant 0.22
PPE35 2167771 p.Ser948Cys missense_variant 0.43
PPE35 2168656 p.Asn653Tyr missense_variant 0.36
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169092 c.1521G>T synonymous_variant 0.18
PPE35 2169317 p.Phe432Leu missense_variant 0.22
PPE35 2169405 p.Asn403Ile missense_variant 0.4
PPE35 2170414 p.Ala67Pro missense_variant 0.25
Rv1979c 2222908 p.Phe86Tyr missense_variant 0.29
Rv1979c 2223057 c.108A>T synonymous_variant 0.5
Rv1979c 2223137 p.Ala10Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289702 c.-461T>G upstream_gene_variant 0.2
kasA 2519064 p.Ile317Ser missense_variant 0.17
eis 2715494 c.-162T>G upstream_gene_variant 0.17
folC 2746634 p.Asp322Ala missense_variant 0.43
folC 2746880 p.Lys240Met missense_variant 0.4
folC 2747509 c.90T>A synonymous_variant 0.33
pepQ 2859815 p.Ile202Leu missense_variant 0.33
pepQ 2859895 p.Glu175Ala missense_variant 0.29
pepQ 2859946 p.Val158Gly missense_variant 0.29
ribD 2986699 c.-140T>G upstream_gene_variant 0.12
ribD 2987038 p.Asp67Gly missense_variant 0.23
Rv2752c 3064784 p.Ser470Pro missense_variant 0.22
thyX 3067265 c.681C>T synonymous_variant 0.2
thyA 3073732 p.Val247Asp missense_variant 0.13
thyA 3073844 p.Asp210Asn missense_variant 0.17
thyA 3074477 c.-6T>G upstream_gene_variant 0.43
ald 3087437 p.Gln206His missense_variant 0.3
ald 3087670 p.Asp284Ala missense_variant 0.2
fbiD 3339577 p.Phe154Val missense_variant 0.29
Rv3236c 3612065 p.Val351Gly missense_variant 0.22
Rv3236c 3612984 p.Asn45Tyr missense_variant 0.43
fbiA 3640442 c.-101A>T upstream_gene_variant 0.5
fbiB 3641597 c.63C>A synonymous_variant 0.2
rpoA 3878490 c.18C>G synonymous_variant 0.5
embC 4241679 p.Val606Gly missense_variant 0.38
embC 4241813 p.Ser651Ala missense_variant 0.29
embC 4241971 c.2109T>A synonymous_variant 0.25
embC 4242186 p.Asp775Ala missense_variant 0.18
embC 4242225 p.Asn788Thr missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244362 p.Asn377Thr missense_variant 0.2
embA 4244413 p.Val394Gly missense_variant 0.22
embA 4245342 p.Ser704Ala missense_variant 0.13
embB 4246133 c.-381G>A upstream_gene_variant 1.0
embB 4246630 c.117G>A synonymous_variant 1.0
embB 4247311 c.798C>T synonymous_variant 0.13
aftB 4268735 c.102C>A synonymous_variant 0.33
ubiA 4269500 p.Thr112Pro missense_variant 0.2
ethA 4326043 c.1431T>G synonymous_variant 0.23
ethA 4327370 p.Leu35Gln missense_variant 0.27
ethA 4327449 p.Ile9Phe missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0