TB-Profiler result

Run: ERR11050234
Summary

Run ID: ERR11050234

Sample name:

Date: 02-04-2023 17:26:06

Number of reads: 778986

Percentage reads mapped: 99.5

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 0.99
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 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 7144 p.Gln635His missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8050 p.Ser250Phe missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9387 p.Ala696Thr missense_variant 0.14
gyrA 9649 p.Val783Gly missense_variant 0.2
fgd1 491315 p.Gly178Ala missense_variant 0.29
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576116 p.Ala257Pro missense_variant 0.5
mshA 576337 c.990G>A synonymous_variant 0.14
mshA 576606 p.Ala420Gly missense_variant 0.5
ccsA 620019 c.129A>T synonymous_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761161 p.Leu452Arg missense_variant 0.18
rpoC 764367 p.Gly333Ala missense_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765479 p.Tyr704Asn missense_variant 0.2
rpoC 765507 p.Val713Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775937 c.2544G>T synonymous_variant 0.15
mmpL5 777169 p.Phe438Ile missense_variant 0.2
mmpL5 777883 p.Gly200Arg missense_variant 0.57
mmpR5 778181 c.-809C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416430 c.918G>C synonymous_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.24
fabG1 1673553 p.Asp38Glu missense_variant 0.25
fabG1 1674065 p.Lys209Thr missense_variant 0.18
inhA 1674838 p.Ala213Thr missense_variant 0.18
rpsA 1833373 c.-169G>A upstream_gene_variant 0.12
rpsA 1833829 p.Lys96Asn missense_variant 0.2
rpsA 1834712 p.Ile391Val missense_variant 1.0
tlyA 1917960 c.21T>G synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918087 p.Thr50Pro missense_variant 0.67
ndh 2102140 c.903C>T synonymous_variant 0.15
PPE35 2168156 c.2457A>C synonymous_variant 0.33
PPE35 2168564 c.2049T>C synonymous_variant 0.11
PPE35 2169938 c.675C>G synonymous_variant 0.12
PPE35 2170013 c.600C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290046 c.-805A>T upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714537 p.Ser266Gly missense_variant 0.15
eis 2715237 c.96A>C synonymous_variant 0.21
folC 2746236 p.Asp455Asn missense_variant 0.13
pepQ 2859933 c.486C>G synonymous_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.4
Rv2752c 3064823 p.Val457Leu missense_variant 0.12
thyX 3067944 p.Val1Gly missense_variant 0.67
thyA 3074318 p.Phe52Leu missense_variant 0.1
thyA 3074490 c.-19G>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449632 c.1129C>T synonymous_variant 0.11
Rv3083 3449856 p.Met451Ile missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840357 p.Leu355Arg missense_variant 0.17
rpoA 3878552 c.-45C>T upstream_gene_variant 0.18
clpC1 4040550 p.Leu52Trp missense_variant 0.33
embC 4242558 p.Gln899Leu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242744 p.Thr961Ile missense_variant 0.12
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.3
embA 4244209 p.Leu326Gln missense_variant 0.17
embB 4247013 p.Pro167Arg missense_variant 1.0
embB 4247100 p.Ala196Val missense_variant 0.22
embB 4247900 c.1387C>T synonymous_variant 0.12
embB 4248134 p.Phe541Val missense_variant 0.12
embB 4248328 c.1815G>C synonymous_variant 0.15
aftB 4267400 c.1437G>C synonymous_variant 0.29
ethR 4328039 p.Arg164Pro missense_variant 0.29
whiB6 4338200 p.Asp108His missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 1.0
gid 4408405 c.-203G>A upstream_gene_variant 0.11