TB-Profiler result

Run: ERR4407548
Summary

Run ID: ERR4407548

Sample name:

Date: 01-04-2023 05:49:32

Number of reads: 329855

Percentage reads mapped: 98.91

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289231 p.Leu4Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 6998 p.Arg587Cys missense_variant 0.11
gyrB 7007 p.Leu590Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8053 p.Ile251Thr missense_variant 0.2
gyrA 8530 p.Ala410Glu missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9453 p.Arg718Cys missense_variant 0.15
fgd1 490911 c.129T>C synonymous_variant 0.17
fgd1 490995 c.213C>T synonymous_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575675 p.Arg110Cys missense_variant 0.11
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 759980 c.174G>A synonymous_variant 0.15
rpoB 760020 p.Gly72Ser missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760420 p.Trp205Leu missense_variant 0.4
rpoB 760935 p.Glu377* stop_gained 0.12
rpoB 761257 c.1455dupG frameshift_variant 0.12
rpoB 762591 p.His929Asn missense_variant 0.17
rpoC 764036 p.Trp223Arg missense_variant 0.13
rpoC 764649 p.Arg427Gln missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765182 p.Asp605Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776055 p.Val809Ala missense_variant 0.18
mmpL5 776473 p.Gln670Lys missense_variant 0.1
mmpL5 777024 p.Arg486Gln missense_variant 0.2
mmpL5 778297 p.Val62Leu missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800968 p.Tyr54Asp missense_variant 0.11
rplC 801095 p.Gln96Arg missense_variant 0.12
fbiC 1303523 p.Trp198Leu missense_variant 0.11
fbiC 1304984 p.Leu685Pro missense_variant 0.18
fbiC 1305053 p.Met708Thr missense_variant 0.15
Rv1258c 1406273 c.1068C>A synonymous_variant 0.14
embR 1416217 c.1131G>A synonymous_variant 0.22
embR 1416911 p.Arg146Leu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918371 c.432C>T synonymous_variant 0.13
ndh 2101896 p.Gly383Ser missense_variant 0.14
ndh 2103225 c.-183A>C upstream_gene_variant 0.2
katG 2154097 p.Pro672Leu missense_variant 0.29
katG 2156271 c.-160G>T upstream_gene_variant 0.15
katG 2156385 c.-274C>T upstream_gene_variant 0.11
PPE35 2168376 p.Thr746Asn missense_variant 0.33
PPE35 2168775 p.Pro613Leu missense_variant 0.29
Rv1979c 2222772 p.Glu131Asp missense_variant 0.18
Rv1979c 2222905 p.Gly87Val missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714655 c.678C>T synonymous_variant 0.15
eis 2715057 c.276C>T synonymous_variant 0.18
eis 2715060 p.His91Met missense_variant 0.2
eis 2715065 p.Thr90Ala missense_variant 0.18
folC 2746350 p.Leu417Met missense_variant 0.11
folC 2746897 c.702C>T synonymous_variant 0.13
folC 2747262 p.Lys113Glu missense_variant 0.18
pepQ 2859598 p.Asp274Ala missense_variant 1.0
pepQ 2860208 p.Leu71Ile missense_variant 0.15
ribD 2986674 c.-165G>A upstream_gene_variant 0.11
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064800 p.Glu464Asp missense_variant 0.4
Rv2752c 3064862 p.Val444Met missense_variant 0.2
Rv2752c 3066312 c.-121C>A upstream_gene_variant 0.12
thyX 3067369 c.577C>A synonymous_variant 0.15
thyA 3074535 c.-64C>T upstream_gene_variant 0.2
Rv3083 3448339 c.-165G>C upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474110 p.Ala35Val missense_variant 0.14
whiB7 3568605 c.75C>T synonymous_variant 0.22
Rv3236c 3612066 p.Val351Phe missense_variant 0.18
Rv3236c 3613226 c.-110G>A upstream_gene_variant 0.12
fbiB 3642121 p.Asp196Gly missense_variant 0.12
fbiB 3642336 p.Thr268Ala missense_variant 0.11
fbiB 3642635 p.Asp367Glu missense_variant 0.15
alr 3840214 p.Arg403Ser missense_variant 0.25
alr 3841540 c.-121_-120insA upstream_gene_variant 0.17
clpC1 4039552 p.Leu385Met missense_variant 0.17
panD 4043879 c.403C>A synonymous_variant 0.17
panD 4043907 c.375C>A synonymous_variant 0.17
embC 4239972 p.Gly37Val missense_variant 0.13
embC 4242360 p.Asn833Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4245563 c.-951G>T upstream_gene_variant 0.14
embA 4245896 p.Tyr888* stop_gained 0.2
embB 4247847 p.Gln445Leu missense_variant 0.17
ethR 4326634 c.-915C>T upstream_gene_variant 0.22
ethA 4326899 p.Pro192Leu missense_variant 0.18
ethR 4327309 c.-240G>A upstream_gene_variant 0.14
ethA 4327716 c.-243G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407530 c.673T>C stop_lost&splice_region_variant 0.12
gid 4408361 c.-159A>G upstream_gene_variant 0.12