TB-Profiler result

Run: ERR2228806
Summary

Run ID: ERR2228806

Sample name:

Date: 31-03-2023 16:21:35

Number of reads: 564084

Percentage reads mapped: 99.29

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 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
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 5536 c.297G>T synonymous_variant 0.25
gyrB 7083 p.Glu615Val missense_variant 0.22
gyrB 7094 p.Lys619* stop_gained 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7738 p.Asp146Ala missense_variant 0.25
gyrA 7948 p.Leu216Gln missense_variant 0.29
fgd1 490590 c.-193A>C upstream_gene_variant 0.25
fgd1 490781 c.-2T>A upstream_gene_variant 0.42
mshA 576074 p.Asp243Tyr missense_variant 0.2
mshA 576477 p.Leu377Arg missense_variant 0.18
ccsA 619844 c.-47T>G upstream_gene_variant 0.4
rpoB 762328 p.Val841Gly missense_variant 0.43
rpoB 762745 p.Gln980Leu missense_variant 0.43
rpoC 763360 c.-10A>T upstream_gene_variant 0.29
rpoC 764708 p.Met447Leu missense_variant 0.36
rpoC 765273 p.Val635Ala missense_variant 0.2
rpoC 766794 p.Tyr1142Ser missense_variant 0.15
rpoC 766926 p.Phe1186Cys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776427 p.Asn685Thr missense_variant 0.18
mmpL5 776449 p.Glu678Gln missense_variant 0.17
mmpL5 777592 p.Ser297Ala missense_variant 0.29
mmpL5 778204 p.Ile93Phe missense_variant 0.18
mmpS5 778625 p.Thr94Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 0.94
fbiC 1303545 p.Lys205Asn missense_variant 0.33
fbiC 1303607 p.Lys226Met missense_variant 0.29
fbiC 1303613 p.Leu228Pro missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303808 p.Gln293Leu missense_variant 0.22
fbiC 1305033 c.2103T>G synonymous_variant 0.15
Rv1258c 1406130 p.Asp404Val missense_variant 0.2
Rv1258c 1406558 c.783T>C synonymous_variant 0.5
Rv1258c 1406583 p.Asp253Ala missense_variant 0.67
Rv1258c 1406972 c.369T>G synonymous_variant 0.17
Rv1258c 1407039 p.Val101Gly missense_variant 0.4
embR 1417516 c.-169T>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.67
rrl 1473459 n.-199G>T upstream_gene_variant 0.38
rrl 1473903 n.246A>T non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474161 n.504A>C non_coding_transcript_exon_variant 0.33
rrl 1474175 n.518A>T non_coding_transcript_exon_variant 0.4
rrl 1474321 n.664T>C non_coding_transcript_exon_variant 0.29
rrl 1474806 n.1149A>T non_coding_transcript_exon_variant 0.29
rrl 1474914 n.1257A>T non_coding_transcript_exon_variant 0.4
rrl 1476067 n.2410A>T non_coding_transcript_exon_variant 0.5
rrl 1476579 n.2922T>A non_coding_transcript_exon_variant 0.33
rrl 1476692 n.3035T>A non_coding_transcript_exon_variant 0.25
inhA 1674655 p.Ser152Arg missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918558 p.Ser207Ala missense_variant 0.31
tlyA 1918607 p.Val223Gly missense_variant 0.36
ndh 2101703 p.Glu447Ala missense_variant 0.38
katG 2155785 c.327T>C synonymous_variant 0.18
katG 2155897 p.Asp72Ala missense_variant 0.22
PPE35 2167969 p.Pro882Thr missense_variant 0.4
PPE35 2168265 p.Gly783Val missense_variant 0.33
PPE35 2168657 c.1956T>A synonymous_variant 0.33
PPE35 2168661 p.Ile651Lys missense_variant 0.4
PPE35 2168675 c.1938T>A synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168943 p.Gln557Leu missense_variant 0.4
PPE35 2169215 p.Glu466Asp missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170056 p.Val186Gly missense_variant 0.33
PPE35 2170153 p.Tyr154Asp missense_variant 0.29
PPE35 2170336 p.Met93Leu missense_variant 0.18
PPE35 2170601 c.12A>T synonymous_variant 0.18
Rv1979c 2221762 p.Tyr468Phe missense_variant 0.18
Rv1979c 2221962 c.1203A>T synonymous_variant 0.43
Rv1979c 2222588 p.Tyr193Asn missense_variant 0.33
Rv1979c 2223070 p.Ile32Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.17
pncA 2289654 c.-413A>C upstream_gene_variant 0.4
kasA 2518066 c.-49A>G upstream_gene_variant 0.22
kasA 2519062 c.948T>G synonymous_variant 0.14
kasA 2519097 p.Val328Gly missense_variant 0.2
ahpC 2725965 c.-228T>A upstream_gene_variant 0.25
ahpC 2726303 c.111T>A synonymous_variant 0.36
ahpC 2726318 p.Glu42Asp missense_variant 0.25
ahpC 2726320 p.His43Pro missense_variant 0.25
ahpC 2726341 p.Val50Glu missense_variant 0.5
ahpC 2726428 p.Asp79Ala missense_variant 0.4
folC 2746439 p.Val387Glu missense_variant 0.29
folC 2747036 p.Asn188Thr missense_variant 0.5
folC 2747695 c.-97C>T upstream_gene_variant 0.15
pepQ 2860192 p.Glu76Ala missense_variant 0.25
ribD 2986662 c.-177T>G upstream_gene_variant 0.33
ribD 2987086 p.Val83Gly missense_variant 0.5
Rv2752c 3065496 c.696G>T synonymous_variant 0.29
thyX 3067363 p.Phe195Ile missense_variant 0.18
thyX 3067863 p.Asp28Ala missense_variant 0.6
thyX 3068104 c.-159C>A upstream_gene_variant 0.5
ald 3087619 p.Ile267Lys missense_variant 0.21
ald 3087928 p.Leu370Arg missense_variant 0.22
fbiD 3339230 p.Val38Gly missense_variant 0.35
fbiD 3339744 c.627A>C synonymous_variant 0.2
fprA 3474507 c.501C>A synonymous_variant 0.33
whiB7 3568462 p.Gln73Leu missense_variant 0.2
Rv3236c 3612572 p.Val182Gly missense_variant 0.5
Rv3236c 3612581 p.Leu179Arg missense_variant 0.6
Rv3236c 3612643 p.Glu158Asp missense_variant 0.4
Rv3236c 3613138 c.-22A>T upstream_gene_variant 0.4
fbiA 3640512 c.-31T>C upstream_gene_variant 0.25
fbiB 3641911 p.Asp126Ala missense_variant 0.18
fbiB 3642047 c.513G>C synonymous_variant 0.18
fbiB 3642060 p.Tyr176Asn missense_variant 0.22
fbiB 3642498 p.Thr322Pro missense_variant 0.29
alr 3841595 c.-175T>A upstream_gene_variant 0.2
ddn 3987059 c.216G>T synonymous_variant 0.23
clpC1 4040170 p.Thr179Pro missense_variant 0.18
clpC1 4040259 p.Glu149Ala missense_variant 0.5
embC 4241450 p.Ser530Ala missense_variant 0.25
embC 4242032 p.Thr724Pro missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244298 p.Ser356Ala missense_variant 0.2
embA 4244308 p.Val359Ala missense_variant 0.2
embA 4244362 p.Asn377Thr missense_variant 0.22
embA 4245066 p.Phe612Ile missense_variant 0.29
embA 4245844 p.Val871Gly missense_variant 0.29
embB 4246589 p.Thr26Pro missense_variant 0.4
embB 4246638 p.Val42Ala missense_variant 0.3
embB 4247039 p.Phe176Val missense_variant 0.2
embB 4249182 p.His890Pro missense_variant 0.25
aftB 4267203 p.Lys545Met missense_variant 0.18
aftB 4268253 p.Leu195Arg missense_variant 0.27
aftB 4268865 c.-29T>G upstream_gene_variant 0.4
ethA 4327366 p.Glu36Asp missense_variant 0.29
ethR 4328021 p.Asp158Ala missense_variant 0.17
ethA 4328324 c.-851A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338676 c.-155T>G upstream_gene_variant 0.25
gid 4407973 p.Val77Gly missense_variant 0.38
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0