TB-Profiler result

Run: ERR4827453
Summary

Run ID: ERR4827453

Sample name:

Date: 01-04-2023 18:04:16

Number of reads: 1095689

Percentage reads mapped: 99.49

Strain: lineage4.1.2.1

Drug-resistance: Other

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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 0.99
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.45 streptomycin
gid 4407846 c.355_356delGC frameshift_variant 1.0 streptomycin
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 5947 c.708C>A synonymous_variant 0.2
gyrB 7139 p.Arg634Ser missense_variant 0.15
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
mshA 575697 p.Phe117Ser missense_variant 0.12
mshA 576111 p.Ala255Gly missense_variant 0.25
mshA 576607 c.1260G>T synonymous_variant 0.17
ccsA 620628 c.738C>T synonymous_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760302 p.Glu166Lys missense_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.15
rpoC 765016 c.1647C>A synonymous_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765484 c.2115G>C synonymous_variant 0.12
rpoC 766800 p.Ala1144Gly missense_variant 0.13
rpoC 766963 c.3594T>G synonymous_variant 0.33
rpoC 766967 p.Pro1200Thr missense_variant 0.25
rpoC 767041 c.3672G>A synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775981 p.Leu834Met missense_variant 0.33
mmpL5 775987 p.His832Tyr missense_variant 0.22
mmpL5 775990 c.2491C>T synonymous_variant 0.18
mmpL5 777062 c.1418delT frameshift_variant 0.22
mmpL5 777729 p.Gly251Ala missense_variant 0.22
mmpL5 778280 p.Asp67Glu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801079 p.Ala91Ser missense_variant 0.2
rplC 801116 p.Ala103Glu missense_variant 0.14
fbiC 1303711 p.Val261Leu missense_variant 0.2
fbiC 1304358 p.Ile476Met missense_variant 0.12
fbiC 1304569 p.Val547Leu missense_variant 0.15
Rv1258c 1406275 p.Ala356Pro missense_variant 0.13
Rv1258c 1407079 c.261delC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471823 n.-23C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
fabG1 1673828 p.Asn130Ser missense_variant 0.13
fabG1 1674106 p.Phe223Leu missense_variant 0.15
inhA 1674660 c.459G>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101721 p.Arg441Leu missense_variant 0.2
ndh 2102885 p.Pro53Leu missense_variant 0.13
katG 2156404 c.-293G>A upstream_gene_variant 0.13
PPE35 2167674 p.Leu980Arg missense_variant 0.34
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289238 p.Arg2Trp missense_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518807 c.693C>T synonymous_variant 0.13
kasA 2519041 c.927C>T synonymous_variant 0.12
eis 2715022 p.Leu104Gln missense_variant 0.13
folC 2747272 c.327G>T synonymous_variant 0.2
pepQ 2859352 p.Gly356Glu missense_variant 0.15
ribD 2987509 p.Ala224Glu missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087390 p.Gly191Ser missense_variant 0.15
fbiD 3339143 c.28_35delATCGGCTT frameshift_variant 0.18
fbiD 3339156 c.40_41insAGCCGATA frameshift_variant 0.17
Rv3083 3449397 c.894C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612360 p.Gly253Trp missense_variant 0.15
fbiA 3640471 c.-72G>A upstream_gene_variant 0.14
fbiB 3641730 p.Asp66Tyr missense_variant 0.13
fbiB 3641999 c.465_466insAGGA frameshift_variant 0.25
fbiB 3642204 p.Asp224His missense_variant 0.18
fbiB 3642388 p.Thr285Ser missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.4
embC 4242010 c.2148G>A synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243724 c.492G>A synonymous_variant 0.22
embA 4244184 p.Ser318Leu missense_variant 0.25
embA 4246038 p.Ala936Thr missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.45
embB 4246556 p.Ala15Pro missense_variant 0.45
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247053 c.540C>T synonymous_variant 0.29
embB 4247059 c.546C>G synonymous_variant 0.29
embB 4247060 p.Pro183Ala missense_variant 0.29
embB 4247066 p.Ile185Val missense_variant 0.29
embB 4249235 p.Gly908Arg missense_variant 0.12
aftB 4266985 p.Pro618Ser missense_variant 0.12
ubiA 4269422 p.Tyr138Asn missense_variant 0.15
ethR 4326844 c.-705G>C upstream_gene_variant 0.22
ethA 4326952 p.Asp174Glu missense_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.19
ethA 4328368 c.-895G>T upstream_gene_variant 0.15
whiB6 4338214 p.Gly103Asp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0