TB-Profiler result

Run: ERR1274697
Summary

Run ID: ERR1274697

Sample name:

Date: 31-03-2023 13:29:06

Number of reads: 305987

Percentage reads mapped: 99.48

Strain: lineage4.1.1

Drug-resistance: HR-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 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, 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 5578 c.339G>A synonymous_variant 0.11
gyrB 6687 p.Gly483Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576453 p.Val369Ala missense_variant 0.2
ccsA 619910 p.Asn7Ser missense_variant 0.4
ccsA 620517 c.627A>G synonymous_variant 0.18
rpoB 760493 c.687C>A synonymous_variant 1.0
rpoB 761147 c.1341C>T synonymous_variant 1.0
rpoB 761258 p.Glu484Asp missense_variant 0.12
rpoC 764626 c.1257C>A synonymous_variant 0.13
rpoC 764994 p.Ala542Val missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765719 p.Glu784Gln missense_variant 1.0
rpoC 766070 c.2701C>T synonymous_variant 1.0
rpoC 767009 p.Ser1214Pro missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776835 p.Val549Asp missense_variant 0.13
mmpL5 777184 p.Ala433Thr missense_variant 0.14
mmpL5 777947 c.534G>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.27
Rv1258c 1406807 c.534G>T synonymous_variant 0.2
embR 1416554 p.Ser265Phe missense_variant 0.12
embR 1416689 p.Arg220Gln missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474652 n.995T>C non_coding_transcript_exon_variant 0.15
rrl 1476125 n.2468G>T non_coding_transcript_exon_variant 0.17
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
rpsA 1833688 c.147C>T synonymous_variant 0.12
rpsA 1833765 c.228delC frameshift_variant 0.1
rpsA 1834599 p.Leu353Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102010 p.Ser345Gly missense_variant 0.12
ndh 2102346 p.Ala233Thr missense_variant 0.2
katG 2156321 c.-210A>T upstream_gene_variant 0.25
PPE35 2169396 p.Gly406Asp missense_variant 0.17
PPE35 2169596 p.Phe339Val missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.13
kasA 2518609 p.Met165Ile missense_variant 0.14
folC 2746766 p.Gln278Arg missense_variant 0.33
Rv2752c 3064836 p.Leu452Phe missense_variant 0.14
Rv2752c 3065143 p.Gly350Glu missense_variant 0.25
thyX 3067717 p.Ser77Gly missense_variant 0.13
thyA 3074169 p.Trp101Cys missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086828 c.9C>T synonymous_variant 0.15
fbiD 3339661 p.Trp182Arg missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475248 c.1242G>A synonymous_variant 0.17
Rv3236c 3613150 c.-34G>A upstream_gene_variant 0.12
fbiA 3640655 p.Asp38Gly missense_variant 0.15
fbiB 3641205 c.-330C>T upstream_gene_variant 0.12
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642846 p.Pro438Thr missense_variant 0.14
alr 3840490 p.Pro311Ser missense_variant 0.13
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878038 p.Ala157Val missense_variant 0.13
clpC1 4039064 c.1641C>T synonymous_variant 0.11
clpC1 4040164 p.Ala181Ser missense_variant 0.15
embC 4240628 p.Gly256Ser missense_variant 0.4
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241144 p.Ala428Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243070 p.Ala1070Thr missense_variant 0.12
embB 4248399 p.Leu629Pro missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
ethR 4327931 p.Arg128Lys missense_variant 0.18
ethR 4328038 p.Arg164Cys missense_variant 0.22
ethA 4328275 c.-802G>A upstream_gene_variant 0.22
ethA 4328398 c.-925C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0