TB-Profiler result

Run: ERR7801202
Summary

Run ID: ERR7801202

Sample name:

Date: 02-04-2023 05:58:46

Number of reads: 732107

Percentage reads mapped: 99.22

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 2155581 c.530delG frameshift_variant 0.11 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 6140 p.Val301Leu missense_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8988 p.Thr563Ala missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575160 c.-187delT upstream_gene_variant 0.14
ccsA 619791 c.-100G>T upstream_gene_variant 0.18
ccsA 620039 p.Pro50Gln missense_variant 0.18
ccsA 620100 c.210G>T synonymous_variant 0.14
ccsA 620605 c.719delT frameshift_variant 0.17
ccsA 620617 p.Gly243Arg missense_variant 0.18
ccsA 620620 p.Val244Leu missense_variant 0.14
rpoB 761255 c.1449T>C synonymous_variant 0.12
rpoB 762357 p.Asp851Tyr missense_variant 0.17
rpoB 762386 c.2581dupG frameshift_variant 0.25
rpoB 762825 p.Gly1007Trp missense_variant 0.17
rpoC 764543 p.Thr392Ala missense_variant 0.15
rpoC 764582 p.Leu405Met missense_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 0.17
mmpL5 776002 p.Leu827Met missense_variant 0.15
mmpL5 778489 c.-9G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302885 c.-46G>T upstream_gene_variant 0.17
fbiC 1302969 c.39G>T synonymous_variant 0.23
fbiC 1305088 p.Val720Phe missense_variant 0.13
Rv1258c 1407473 c.-133C>A upstream_gene_variant 0.22
Rv1258c 1407537 c.-197G>A upstream_gene_variant 0.17
embR 1417098 p.Gly84Cys missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472152 n.307C>A non_coding_transcript_exon_variant 0.18
rrs 1472155 n.310C>A non_coding_transcript_exon_variant 0.18
rrl 1474042 n.385G>T non_coding_transcript_exon_variant 0.17
rrl 1474736 n.1083_1084delGG non_coding_transcript_exon_variant 0.17
rrl 1475766 n.2109G>T non_coding_transcript_exon_variant 0.22
fabG1 1673588 p.Gly50Val missense_variant 0.25
fabG1 1674133 p.Ile232Val missense_variant 0.1
inhA 1674680 p.Trp160Leu missense_variant 0.18
inhA 1674729 c.528G>T synonymous_variant 0.17
tlyA 1917838 c.-102G>T upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918301 p.Ser121* stop_gained 0.2
tlyA 1918723 p.Arg262Ser missense_variant 0.2
katG 2155743 c.369G>T synonymous_variant 0.17
PPE35 2170666 c.-54G>A upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289962 c.-721C>A upstream_gene_variant 0.15
pncA 2289982 c.-741C>A upstream_gene_variant 0.15
kasA 2518882 c.768C>A synonymous_variant 0.18
eis 2714513 p.Pro274Thr missense_variant 0.22
eis 2714871 c.462G>T synonymous_variant 0.17
folC 2746709 p.His297Arg missense_variant 0.12
folC 2746929 p.Pro224Thr missense_variant 0.2
Rv2752c 3065566 p.Pro209His missense_variant 0.27
Rv2752c 3067082 c.-891C>A upstream_gene_variant 0.17
thyX 3067277 c.669C>A synonymous_variant 0.22
thyX 3067838 c.108C>A synonymous_variant 0.2
thyA 3073847 p.Tyr209His missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339318 c.201C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611966 p.Ser384* stop_gained 0.29
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612076 c.1041G>T synonymous_variant 0.2
Rv3236c 3612084 p.Gly345Cys missense_variant 0.22
Rv3236c 3612085 c.1032C>T synonymous_variant 0.22
Rv3236c 3612100 c.1017C>A synonymous_variant 0.2
Rv3236c 3612240 p.Val293Leu missense_variant 0.13
fbiA 3641333 p.Gly264Val missense_variant 0.18
alr 3840569 c.852G>T synonymous_variant 0.18
alr 3840621 p.Gly267Asp missense_variant 0.22
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840847 p.Gly192Arg missense_variant 0.14
alr 3840869 c.552C>A synonymous_variant 0.24
rpoA 3877512 c.996C>A synonymous_variant 0.17
rpoA 3878048 p.Ala154Ser missense_variant 0.14
rpoA 3878406 c.102G>T synonymous_variant 0.18
ddn 3987277 p.Pro145Gln missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038607 p.Glu700* stop_gained 0.2
clpC1 4039040 c.1665C>A synonymous_variant 0.17
clpC1 4039400 p.Lys435Asn missense_variant 0.15
clpC1 4039925 c.780C>A synonymous_variant 0.15
panD 4044045 c.237G>A synonymous_variant 0.17
embC 4240539 p.Pro226His missense_variant 0.17
embC 4240714 p.Trp284Cys missense_variant 0.14
embC 4241173 p.Phe437Leu missense_variant 0.17
embC 4241175 p.Ser438Tyr missense_variant 0.17
embA 4242292 c.-941C>T upstream_gene_variant 0.17
embC 4242345 p.Ala828Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243034 p.Gly1058Cys missense_variant 0.19
embA 4243157 c.-76G>A upstream_gene_variant 0.2
embA 4243543 p.Gly104Val missense_variant 0.17
embA 4244189 c.957C>A synonymous_variant 0.18
embA 4244539 p.Ala436Val missense_variant 0.17
embA 4244780 c.1548C>A synonymous_variant 0.2
embA 4244942 p.Trp570Cys missense_variant 0.2
embA 4245012 p.Arg594Ser missense_variant 0.17
embA 4245729 p.Asp833Tyr missense_variant 0.15
embB 4245755 c.-759C>A upstream_gene_variant 0.2
embB 4245791 c.-723C>A upstream_gene_variant 0.2
embA 4246035 p.Glu935* stop_gained 0.4
embB 4247027 p.Leu172Met missense_variant 0.27
embB 4247207 p.Ala232Pro missense_variant 1.0
aftB 4267983 p.Arg285His missense_variant 0.15
aftB 4268011 p.Leu276Met missense_variant 0.13
aftB 4268169 p.Ala223Asp missense_variant 0.15
aftB 4268672 c.165C>A synonymous_variant 0.29
aftB 4268856 c.-20C>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408459 c.-257G>C upstream_gene_variant 0.12
PPE35 2158030 c.-22_*9618del transcript_ablation 1.0