TB-Profiler result

Run: ERR4407530
Summary

Run ID: ERR4407530

Sample name:

Date: 01-04-2023 05:48:44

Number of reads: 469168

Percentage reads mapped: 99.38

Strain: lineage4.1.2.1

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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
katG 2154100 p.Ser671* stop_gained 0.2 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5571 p.Ser111* stop_gained 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.43
rpoB 759979 p.Leu58Gln missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761776 p.Asp657Gly missense_variant 0.11
rpoC 764272 c.903G>A synonymous_variant 0.17
rpoC 765020 p.Ala551Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765491 p.Val708Met missense_variant 0.12
rpoC 766096 c.2730_2755delGATCCGCGACCCGTACATCGAAACCT frameshift_variant 0.11
rpoC 766267 c.2899_2902delACGT frameshift_variant 0.17
rpoC 766275 p.Ala969Gly missense_variant 0.17
rpoC 766278 c.2909_2910insACGT frameshift_variant 0.17
rpoC 767091 p.Arg1241Leu missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776313 p.Glu723Val missense_variant 0.1
mmpL5 778840 c.-360C>A upstream_gene_variant 0.12
mmpS5 779496 c.-591G>T upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781666 p.Arg36His missense_variant 0.12
fbiC 1305368 p.Glu813Val missense_variant 0.11
Rv1258c 1407189 p.Thr51Ile missense_variant 0.12
atpE 1461083 c.39T>G synonymous_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.1
rrs 1472486 n.641A>T non_coding_transcript_exon_variant 0.12
rrl 1474177 n.521_522delAC non_coding_transcript_exon_variant 0.13
rrl 1475255 n.1598C>T non_coding_transcript_exon_variant 0.25
rrl 1475462 n.1805G>T non_coding_transcript_exon_variant 0.12
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.11
fabG1 1673441 p.Val1Ala missense_variant 0.13
fabG1 1673872 p.Trp145Arg missense_variant 0.12
inhA 1674912 c.711G>T synonymous_variant 0.18
inhA 1674932 p.Ala244Glu missense_variant 0.2
rpsA 1834712 p.Ile391Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918318 p.Arg127Trp missense_variant 0.11
tlyA 1918345 p.Ala136Ser missense_variant 0.1
katG 2154058 p.Gly685Val missense_variant 0.25
katG 2154593 p.Val507Phe missense_variant 0.2
katG 2154797 p.Gln439Lys missense_variant 0.11
PPE35 2167869 p.Gly915Val missense_variant 0.11
PPE35 2170559 c.54G>A synonymous_variant 0.12
Rv1979c 2222609 p.Thr186Ser missense_variant 0.12
Rv1979c 2222637 c.528A>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289386 c.-145A>T upstream_gene_variant 0.17
pncA 2290057 c.-816G>A upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518505 p.Ala131Ser missense_variant 0.2
folC 2747057 p.Trp181Leu missense_variant 0.29
pepQ 2860164 c.255C>T synonymous_variant 0.12
Rv2752c 3064530 c.1662G>C synonymous_variant 0.1
Rv2752c 3065109 c.1083A>G synonymous_variant 0.14
thyX 3067232 c.714C>A synonymous_variant 0.17
thyX 3067256 p.Phe230Leu missense_variant 0.12
thyX 3067310 c.636C>A synonymous_variant 0.14
thyX 3067467 p.Ala160Glu missense_variant 0.29
thyA 3073719 c.753C>T synonymous_variant 0.12
thyA 3074490 c.-19G>C upstream_gene_variant 1.0
thyA 3074654 c.-183T>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086956 p.Thr46Asn missense_variant 0.15
ald 3086987 p.Gln56His missense_variant 0.15
ald 3087202 p.Pro128Leu missense_variant 0.14
Rv3083 3449276 p.Cys258Phe missense_variant 0.12
Rv3083 3449700 c.1197C>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474013 p.Pro3Thr missense_variant 0.22
Rv3236c 3612359 p.Gly253Val missense_variant 0.15
Rv3236c 3612989 p.Leu43Ser missense_variant 0.14
rpoA 3878071 p.Tyr146Phe missense_variant 0.12
ddn 3987013 c.172delC frameshift_variant 0.14
clpC1 4039484 c.1221T>G synonymous_variant 0.11
clpC1 4039556 c.1149G>A synonymous_variant 0.17
clpC1 4040080 c.624delC frameshift_variant 0.11
panD 4044270 c.12G>A synonymous_variant 0.12
panD 4044291 c.-10G>C upstream_gene_variant 0.14
embC 4241604 c.1744_1745dupAC frameshift_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243019 c.3159delG frameshift_variant 0.14
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.18
embC 4243092 p.Leu1077Arg missense_variant 0.18
embC 4243095 p.Gly1078Val missense_variant 0.18
embA 4243099 c.-134G>C upstream_gene_variant 0.18
embA 4243102 c.-131G>T upstream_gene_variant 0.18
embC 4243103 p.Thr1081Pro missense_variant 0.18
embC 4243106 p.Arg1082Ser missense_variant 0.17
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.15
embB 4247013 p.Pro167Arg missense_variant 1.0
embB 4247153 p.Pro214Ala missense_variant 0.17
ethA 4327080 p.Glu132Lys missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338703 c.-182T>C upstream_gene_variant 0.12
gid 4408094 p.Gly37Arg missense_variant 1.0