TB-Profiler result

Run: ERR2229312

Summary

Run ID: ERR2229312

Sample name:

Date: 31-03-2023 16:59:33

Number of reads: 760708

Percentage reads mapped: 98.63

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 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
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 5860 c.621C>T synonymous_variant 0.15
gyrA 7307 c.6A>G synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8465 c.1164C>T synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576516 p.Val390Gly missense_variant 0.17
ccsA 620240 p.Thr117Asn missense_variant 0.25
ccsA 620599 p.Phe237Leu missense_variant 0.33
rpoB 759966 p.Ser54Thr missense_variant 0.22
rpoB 762176 c.2370T>A synonymous_variant 0.12
rpoC 762929 c.-441G>A upstream_gene_variant 0.13
rpoC 763571 p.Val68Leu missense_variant 0.17
rpoC 764969 p.Ala534Ser missense_variant 0.22
rpoC 766672 p.Asp1101Glu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775693 p.Ala930Thr missense_variant 0.14
mmpL5 776852 c.1629C>A synonymous_variant 0.18
mmpL5 777149 p.Asn444Lys missense_variant 0.2
mmpL5 777157 c.1324C>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.2
mmpL5 778201 p.Val94Met missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304220 c.1290G>A synonymous_variant 0.13
Rv1258c 1407487 c.-147C>A upstream_gene_variant 0.14
Rv1258c 1407540 c.-200C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472536 n.691G>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474489 n.832T>C non_coding_transcript_exon_variant 0.11
rrl 1474597 n.940T>G non_coding_transcript_exon_variant 0.2
fabG1 1673346 c.-94C>G upstream_gene_variant 0.19
fabG1 1673349 c.-91G>C upstream_gene_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
fabG1 1674120 p.Glu227Asp missense_variant 0.17
inhA 1674791 p.Leu197Arg missense_variant 0.15
inhA 1674793 p.Ala198Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918310 p.Asn124Ile missense_variant 0.15
tlyA 1918445 p.Gly169Glu missense_variant 0.13
ndh 2102802 p.Asn81Tyr missense_variant 0.12
katG 2156224 c.-113G>T upstream_gene_variant 0.12
PPE35 2167833 p.Leu927Arg missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168129 c.2484G>T synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169293 c.1320T>C synonymous_variant 0.21
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289266 c.-25A>G upstream_gene_variant 0.15
kasA 2518119 p.Ser2Asn missense_variant 0.14
eis 2714961 c.372C>T synonymous_variant 0.18
pepQ 2859634 p.Gln262Arg missense_variant 0.18
pepQ 2860154 p.Glu89Gln missense_variant 0.2
pepQ 2860467 c.-49G>A upstream_gene_variant 0.13
ribD 2986921 c.88delC frameshift_variant 0.5
ribD 2987448 p.Glu204* stop_gained 0.13
Rv2752c 3064576 p.Lys539Met missense_variant 0.22
Rv2752c 3064727 p.Ala489Ser missense_variant 0.22
Rv2752c 3064971 c.1221C>T synonymous_variant 0.22
fprA 3474217 p.Ala71Thr missense_variant 0.12
fprA 3475224 c.1218G>T synonymous_variant 0.13
whiB7 3568548 c.132G>C synonymous_variant 0.22
Rv3236c 3612202 p.Lys305Asn missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.31
clpC1 4038614 c.2091C>T synonymous_variant 0.17
clpC1 4038675 p.Val677Asp missense_variant 0.2
clpC1 4039018 p.Ser563Ala missense_variant 0.17
clpC1 4039022 c.1683A>G synonymous_variant 0.15
clpC1 4039670 c.1035G>T synonymous_variant 0.13
clpC1 4039829 p.Leu292Ile missense_variant 0.25
embC 4241995 c.2133C>A synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242984 p.Arg1041Leu missense_variant 0.2
embA 4245427 p.Ser732Asn missense_variant 0.17
embA 4245752 p.Met840Ile missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4246834 c.321G>A synonymous_variant 0.12
aftB 4268596 p.Tyr81His missense_variant 0.22
aftB 4268697 p.Pro47Gln missense_variant 0.15
ubiA 4269352 p.Ala161Asp missense_variant 0.14
ubiA 4269756 p.Trp26Cys missense_variant 0.22
ethA 4326092 p.Tyr461Phe missense_variant 0.22
ethA 4327418 p.Ala19Val missense_variant 1.0
ethR 4327640 p.Ala31Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407607 p.Pro199His missense_variant 0.15
gid 4408388 c.-186C>T upstream_gene_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0