TB-Profiler result

Run: ERR10796612
Summary

Run ID: ERR10796612

Sample name:

Date: 31-03-2023 11:12:31

Number of reads: 769034

Percentage reads mapped: 100.0

Strain: lineage4.3.2

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
lineage4.3.2 Euro-American (LAM) LAM3 None 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
katG 2154046 p.Trp689* stop_gained 0.13 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 5882 p.Gln215* stop_gained 0.12
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 491306 p.Ala175Val missense_variant 0.22
fgd1 491352 c.570C>T synonymous_variant 0.15
mshA 575335 c.-13G>C upstream_gene_variant 0.33
mshA 576087 p.Phe247Ser missense_variant 0.12
mshA 576677 p.Ala444Thr missense_variant 1.0
rpoB 762180 p.Asp792Asn missense_variant 0.25
rpoC 762383 c.-987C>T upstream_gene_variant 0.31
rpoB 762501 p.Pro899Ser missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765643 c.2274G>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776356 p.Leu709Val missense_variant 0.18
mmpL5 777459 p.Ile341Asn missense_variant 0.25
mmpL5 777513 p.Cys323Tyr missense_variant 0.13
mmpL5 777546 p.Gly312Asp missense_variant 0.13
mmpL5 778116 p.His122Arg missense_variant 0.12
mmpR5 779192 p.Ser68Asn missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801273 c.465C>T synonymous_variant 0.2
rplC 801443 p.Ile212Asn missense_variant 0.17
fbiC 1303711 p.Val261Ile missense_variant 0.17
fbiC 1303803 c.873C>T synonymous_variant 0.13
fbiC 1303819 p.Ala297Thr missense_variant 0.14
embR 1417032 p.Pro106Ser missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.14
rrs 1473376 n.1531C>A non_coding_transcript_exon_variant 0.14
rrl 1473411 n.-247G>A upstream_gene_variant 0.15
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.12
rrl 1475914 n.2257C>T non_coding_transcript_exon_variant 0.17
rpsA 1834211 p.Ala224Thr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101916 p.Phe376Ser missense_variant 0.13
katG 2154974 p.Thr380Ala missense_variant 0.12
katG 2156139 c.-28G>A upstream_gene_variant 0.11
katG 2156172 c.-61G>A upstream_gene_variant 0.12
Rv1979c 2223243 c.-79G>A upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223334 c.-181_-171delTAGACTCGCGA upstream_gene_variant 1.0
pncA 2289033 p.Pro70Arg missense_variant 0.17
kasA 2518466 p.Gly118Arg missense_variant 0.12
kasA 2519321 p.Gly403Arg missense_variant 0.17
eis 2714243 p.His364Tyr missense_variant 0.3
eis 2714258 p.Leu359Phe missense_variant 0.2
eis 2715300 p.Asp11Glu missense_variant 0.14
folC 2746437 p.Asp388Tyr missense_variant 0.25
folC 2747505 p.His32Tyr missense_variant 0.29
pepQ 2860538 c.-120C>T upstream_gene_variant 0.15
pepQ 2860553 c.-135C>T upstream_gene_variant 0.15
ribD 2986982 c.144C>T synonymous_variant 0.12
ribD 2986989 p.Gly51Ser missense_variant 0.12
ribD 2987178 p.Val114Ile missense_variant 0.12
ribD 2987556 p.Cys240Ser missense_variant 0.29
Rv2752c 3064927 p.Leu422Ser missense_variant 0.15
Rv2752c 3065733 c.459G>A synonymous_variant 0.17
Rv2752c 3065940 c.252G>A synonymous_variant 0.13
Rv2752c 3066159 c.33G>T synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074011 p.Val154Ala missense_variant 0.14
thyA 3074512 c.-41G>A upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086999 c.180C>T synonymous_variant 0.14
ald 3087385 p.Gly189Asp missense_variant 0.15
Rv3083 3448877 p.Thr125Ile missense_variant 0.17
Rv3083 3449697 c.1194G>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474207 c.201C>T synonymous_variant 0.15
whiB7 3568445 p.His79Asn missense_variant 0.15
Rv3236c 3612405 p.Ala238Thr missense_variant 0.12
fbiA 3640987 p.Arg149Gly missense_variant 0.11
fbiA 3641129 p.Ala196Val missense_variant 0.15
fbiA 3641440 p.Gly300Arg missense_variant 0.29
fbiB 3642829 p.Pro432Leu missense_variant 0.17
alr 3840531 p.His297Arg missense_variant 1.0
alr 3841088 c.333C>T synonymous_variant 0.5
alr 3841384 p.Asp13Asn missense_variant 0.12
rpoA 3878027 p.Arg161Cys missense_variant 0.14
rpoA 3878102 p.Val136Ile missense_variant 0.15
rpoA 3878651 c.-144C>T upstream_gene_variant 0.13
ddn 3986799 c.-45G>A upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038443 c.2262G>A synonymous_variant 0.2
clpC1 4038788 c.1917G>A synonymous_variant 0.18
clpC1 4039700 c.1005C>T synonymous_variant 0.15
panD 4044185 p.Met33Leu missense_variant 0.12
embC 4241330 p.Asp490Asn missense_variant 0.33
embC 4241346 p.Gly495Asp missense_variant 0.29
embC 4241357 p.Ala499Thr missense_variant 0.25
embC 4241413 c.1551C>T synonymous_variant 0.18
embC 4241454 p.Ile531Asn missense_variant 0.15
embC 4241860 c.1998C>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243910 c.678G>A synonymous_variant 0.33
embA 4244060 c.828C>T synonymous_variant 0.18
embA 4244745 c.1515delT frameshift_variant 0.13
embB 4246600 c.87G>A synonymous_variant 0.29
embB 4246697 p.Gly62Arg missense_variant 0.4
embB 4246915 c.402C>T synonymous_variant 0.18
embB 4247137 c.624C>A synonymous_variant 0.22
embB 4247974 c.1461C>T synonymous_variant 0.17
embB 4248288 p.Trp592* stop_gained 0.15
embB 4248536 p.Leu675Val missense_variant 0.14
embB 4248826 c.2313G>A synonymous_variant 0.22
aftB 4267826 c.1011G>A synonymous_variant 0.12
aftB 4268408 c.429G>A synonymous_variant 0.12
aftB 4268442 p.Arg132Leu missense_variant 1.0
aftB 4268834 c.3G>A start_lost 0.17
aftB 4268854 c.-18G>A upstream_gene_variant 0.2
ethR 4326712 c.-837C>T upstream_gene_variant 0.12
ethR 4328107 p.Phe187Leu missense_variant 0.12
whiB6 4338242 p.Gln94Glu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408114 p.Gly30Val missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408243 c.-41G>A upstream_gene_variant 0.2