TB-Profiler result

Run: ERR11466072
Summary

Run ID: ERR11466072

Sample name:

Date: 03-01-2024 13:50:45

Number of reads: 4617681

Percentage reads mapped: 99.4

Strain: lineage4.3.4.2.1

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.92
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.98
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 6140 p.Val301Leu missense_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7532 c.231T>G synonymous_variant 0.14
gyrA 7541 c.240C>G synonymous_variant 0.16
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7865 c.564T>C synonymous_variant 0.19
gyrA 8784 p.Arg495Cys missense_variant 1.0
gyrA 9267 p.Asn656Gly missense_variant 0.17
gyrA 9275 c.1974G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575772 p.Val142Ala missense_variant 0.11
mshA 575782 c.435G>C synonymous_variant 0.11
mshA 575785 c.438T>C synonymous_variant 0.11
mshA 575795 p.Ile150Val missense_variant 0.12
mshA 575800 c.453G>C synonymous_variant 0.13
mshA 575803 c.456C>T synonymous_variant 0.15
mshA 575821 c.474G>C synonymous_variant 0.24
mshA 575842 c.495G>C synonymous_variant 0.22
mshA 575864 c.517T>C synonymous_variant 0.16
mshA 575869 c.522G>A synonymous_variant 0.22
ccsA 620649 c.759A>G synonymous_variant 0.12
ccsA 620652 c.762C>G synonymous_variant 0.11
rpoB 760136 c.330G>A synonymous_variant 0.15
rpoB 760139 c.333A>T synonymous_variant 0.15
rpoB 760142 c.336C>G synonymous_variant 0.16
rpoB 760178 c.372G>A synonymous_variant 0.19
rpoB 760181 c.375T>C synonymous_variant 0.22
rpoB 760184 c.378A>G synonymous_variant 0.22
rpoB 760196 c.390C>G synonymous_variant 0.2
rpoB 760235 c.429T>C synonymous_variant 0.13
rpoB 760244 c.438G>C synonymous_variant 0.16
rpoB 760310 c.504G>C synonymous_variant 0.12
rpoB 760424 c.618C>G synonymous_variant 0.13
rpoB 760457 c.651C>T synonymous_variant 0.13
rpoB 761282 c.1476C>T synonymous_variant 0.13
rpoB 761288 c.1482G>T synonymous_variant 0.16
rpoB 761645 c.1839C>G synonymous_variant 0.13
rpoB 761648 c.1842T>C synonymous_variant 0.14
rpoB 761666 c.1860G>C synonymous_variant 0.13
rpoB 761669 c.1863C>T synonymous_variant 0.14
rpoB 762245 c.2439G>C synonymous_variant 0.16
rpoB 762308 c.2502G>C synonymous_variant 0.11
rpoB 762362 p.Glu852Asp missense_variant 0.12
rpoB 762369 c.2563T>C synonymous_variant 0.13
rpoC 762374 c.-996G>C upstream_gene_variant 0.14
rpoB 762879 p.Met1025Leu missense_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.16
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoC 762959 c.-411G>C upstream_gene_variant 0.15
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763570 c.201G>C synonymous_variant 0.14
rpoC 763573 c.204G>C synonymous_variant 0.12
rpoC 763588 c.219C>T synonymous_variant 0.19
rpoC 763594 c.225C>T synonymous_variant 0.17
rpoC 763603 c.234C>T synonymous_variant 0.17
rpoC 763615 c.246G>C synonymous_variant 0.22
rpoC 763618 c.249C>T synonymous_variant 0.24
rpoC 763633 c.264T>C synonymous_variant 0.15
rpoC 763900 c.531G>C synonymous_variant 0.12
rpoC 764344 c.975C>T synonymous_variant 0.16
rpoC 764353 c.984G>T synonymous_variant 0.19
rpoC 764539 c.1170C>G synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.13
rpoC 764758 c.1389C>G synonymous_variant 0.12
rpoC 764764 c.1395T>C synonymous_variant 0.15
rpoC 764827 c.1458G>C synonymous_variant 0.12
rpoC 764858 c.1489T>C synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.94
rpoC 765979 c.2610C>G synonymous_variant 0.14
rpoC 765982 c.2613C>T synonymous_variant 0.14
rpoC 766381 c.3012C>T synonymous_variant 0.14
rpoC 766384 c.3015A>G synonymous_variant 0.15
rpoC 766390 c.3021C>T synonymous_variant 0.16
rpoC 766393 c.3024C>T synonymous_variant 0.85
rpoC 766741 c.3372G>C synonymous_variant 0.12
rpoC 767002 c.3633G>C synonymous_variant 0.2
rpoC 767008 c.3639G>A synonymous_variant 0.19
rpoC 767020 c.3651C>G synonymous_variant 0.17
rpoC 767221 c.3852C>G synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800703 c.-106T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.19
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.14
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.14
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.21
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.24
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.22
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.33
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.3
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.19
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
inhA 1674348 c.147C>T synonymous_variant 0.98
inhA 1674924 c.723G>C synonymous_variant 0.22
inhA 1674930 c.729C>T synonymous_variant 0.22
inhA 1674934 c.733C>T synonymous_variant 0.16
rpsA 1833928 c.387G>C synonymous_variant 0.15
rpsA 1833949 c.408T>C synonymous_variant 0.17
rpsA 1833979 c.438T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155696 p.Ala139Val missense_variant 0.14
katG 2155716 c.396T>G synonymous_variant 0.15
katG 2155722 c.390G>C synonymous_variant 0.15
katG 2155728 c.384G>C synonymous_variant 0.14
katG 2155742 p.Gly124Arg missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518756 c.642G>C synonymous_variant 0.11
kasA 2519077 c.963G>C synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087699 p.Leu294Val missense_variant 0.13
ald 3087704 c.885T>C synonymous_variant 0.15
ald 3087716 c.897G>C synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877638 c.870T>C synonymous_variant 0.14
rpoA 3877905 c.603A>G synonymous_variant 0.13
rpoA 3877908 c.600T>C synonymous_variant 0.13
rpoA 3877920 c.588G>C synonymous_variant 0.12
rpoA 3877926 c.582G>C synonymous_variant 0.16
rpoA 3877962 c.546G>T synonymous_variant 0.14
rpoA 3878160 c.348C>G synonymous_variant 0.19
rpoA 3878163 c.345C>T synonymous_variant 0.21
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038587 c.2118C>G synonymous_variant 0.13
clpC1 4038596 c.2109A>G synonymous_variant 0.17
clpC1 4038602 c.2103G>C synonymous_variant 0.19
clpC1 4038623 c.2082A>G synonymous_variant 0.16
clpC1 4038640 p.Asp689Asn missense_variant 0.15
clpC1 4038647 c.2058T>G synonymous_variant 0.14
clpC1 4038658 p.Lys683Gln missense_variant 0.12
clpC1 4038660 p.Ser682Cys missense_variant 0.12
clpC1 4038662 c.2043T>C synonymous_variant 0.12
clpC1 4038671 c.2034T>G synonymous_variant 0.12
clpC1 4038679 p.Pro676Ala missense_variant 0.16
clpC1 4038683 c.2022T>C synonymous_variant 0.16
clpC1 4038695 c.2010C>G synonymous_variant 0.15
clpC1 4038704 c.2001T>C synonymous_variant 0.13
clpC1 4038710 c.1995G>C synonymous_variant 0.12
clpC1 4038713 c.1992T>C synonymous_variant 0.12
clpC1 4038725 c.1980C>G synonymous_variant 0.14
clpC1 4038842 c.1863G>C synonymous_variant 0.14
clpC1 4038860 c.1845G>C synonymous_variant 0.15
clpC1 4038941 c.1764G>C synonymous_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.13
clpC1 4039064 c.1641C>T synonymous_variant 0.17
clpC1 4039067 c.1638G>C synonymous_variant 0.18
clpC1 4039079 c.1626C>G synonymous_variant 0.13
clpC1 4039085 c.1620A>G synonymous_variant 0.14
clpC1 4039091 c.1614G>C synonymous_variant 0.13
clpC1 4039097 c.1608G>T synonymous_variant 0.13
clpC1 4039103 c.1602T>C synonymous_variant 0.12
clpC1 4039106 c.1599G>C synonymous_variant 0.12
clpC1 4039118 c.1587C>A synonymous_variant 0.14
clpC1 4039142 c.1563A>G synonymous_variant 0.18
clpC1 4039145 c.1560G>C synonymous_variant 0.18
clpC1 4039169 c.1536A>G synonymous_variant 0.16
clpC1 4039178 c.1527G>C synonymous_variant 0.14
clpC1 4039241 c.1464G>C synonymous_variant 0.15
clpC1 4039274 c.1431G>C synonymous_variant 0.12
clpC1 4039286 c.1419T>C synonymous_variant 0.15
clpC1 4040306 c.399G>C synonymous_variant 0.12
clpC1 4040309 c.396C>G synonymous_variant 0.12
clpC1 4040324 c.381G>C synonymous_variant 0.13
clpC1 4040654 c.51G>A synonymous_variant 0.17
clpC1 4040657 c.48T>G synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247527 c.1014G>C synonymous_variant 0.19
embB 4247536 c.1023C>A synonymous_variant 0.16
embB 4247554 c.1041T>C synonymous_variant 0.13
embB 4247555 p.Leu348Ile missense_variant 0.13
whiB6 4338497 p.Ala9Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0