TB-Profiler result

Run: ERR2229323
Summary

Run ID: ERR2229323

Sample name:

Date: 31-03-2023 17:00:58

Number of reads: 620130

Percentage reads mapped: 98.68

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 5146 c.-94A>C upstream_gene_variant 0.14
gyrB 5148 c.-92C>G upstream_gene_variant 0.15
gyrB 5355 p.Glu39Gly missense_variant 0.13
gyrB 6567 p.Ala443Val missense_variant 0.4
gyrB 6651 p.Arg471Leu missense_variant 0.15
gyrB 6653 p.Asp472Tyr missense_variant 0.15
gyrB 7163 c.1924_1925insA frameshift_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7715 c.414G>A synonymous_variant 0.22
gyrA 7837 p.Gly179Val missense_variant 0.22
fgd1 490827 p.Phe15Leu missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.4
ccsA 620042 p.Ala51Asp missense_variant 0.13
rpoB 759951 p.Asp49Asn missense_variant 0.33
rpoB 760180 p.Ala125Val missense_variant 0.33
rpoB 761556 p.Ala584Pro missense_variant 0.2
rpoC 765070 c.1701G>T synonymous_variant 0.29
rpoC 765634 p.Lys755Asn missense_variant 0.15
rpoC 766350 p.Ala994Asp missense_variant 0.22
rpoC 766816 c.3447C>A synonymous_variant 0.2
rpoC 767061 p.Arg1231His missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775713 p.Ser923Trp missense_variant 0.29
mmpL5 775771 p.Ala904Ser missense_variant 0.5
mmpL5 776205 p.Gly759Val missense_variant 0.33
mmpL5 777119 p.His454Gln missense_variant 0.38
mmpL5 777122 c.1359C>T synonymous_variant 0.33
mmpL5 777128 c.1353A>G synonymous_variant 0.25
mmpL5 777185 c.1296G>T synonymous_variant 0.18
mmpL5 777694 p.Thr263Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303113 p.Ser61Arg missense_variant 0.29
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416208 p.Ile380Met missense_variant 0.12
embR 1417112 p.Leu79Pro missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474297 n.640C>A non_coding_transcript_exon_variant 0.17
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.15
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.15
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.15
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.23
fabG1 1673359 c.-81T>C upstream_gene_variant 0.23
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
inhA 1674298 p.Gly33Ser missense_variant 0.4
rpsA 1834061 p.Ile174Phe missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155835 p.Ala93Ser missense_variant 0.22
PPE35 2167997 c.2616G>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169351 p.Ala421Ile missense_variant 0.13
PPE35 2169677 c.936C>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.86
PPE35 2170053 p.Thr187Ser missense_variant 0.83
PPE35 2170238 c.375T>G synonymous_variant 0.11
PPE35 2170395 p.Ala73Val missense_variant 0.15
PPE35 2170403 c.210C>G synonymous_variant 0.14
PPE35 2170406 c.207A>G synonymous_variant 0.14
PPE35 2170413 p.Ala67Gly missense_variant 0.15
PPE35 2170415 c.198A>G synonymous_variant 0.15
PPE35 2170518 p.Asp32Val missense_variant 0.18
PPE35 2170566 p.Phe16Tyr missense_variant 0.25
Rv1979c 2222145 c.1020G>A synonymous_variant 0.17
Rv1979c 2222790 p.Lys125Asn missense_variant 0.2
Rv1979c 2223168 c.-4T>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289053 p.Asp63Glu missense_variant 0.2
pncA 2289383 c.-142G>A upstream_gene_variant 0.12
kasA 2518403 p.Ser97Thr missense_variant 0.22
ahpC 2726581 p.Val130Glu missense_variant 0.25
ahpC 2726678 c.486G>T synonymous_variant 0.18
folC 2747274 p.Ser109Thr missense_variant 0.29
ribD 2987188 c.352delG frameshift_variant 0.67
ribD 2987262 p.Val142Leu missense_variant 0.33
ribD 2987475 p.Leu213Met missense_variant 0.25
thyA 3074595 c.-124C>T upstream_gene_variant 0.2
Rv3236c 3612637 p.Phe160Leu missense_variant 0.4
fbiA 3640668 p.Ser42Arg missense_variant 0.2
fbiA 3640697 p.Trp52* stop_gained 0.17
alr 3841204 p.Gly73Ser missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.24
rpoA 3878044 p.Ser155Leu missense_variant 0.22
rpoA 3878067 c.441C>A synonymous_variant 0.29
ddn 3987220 p.Leu126* stop_gained 0.17
clpC1 4039739 c.943_965delGGTGAACTGCAAACGATCGGCGC frameshift_variant 0.22
clpC1 4039871 c.834C>T synonymous_variant 0.25
clpC1 4039889 c.816G>T synonymous_variant 0.25
clpC1 4039898 c.807C>A synonymous_variant 0.22
clpC1 4040540 c.165G>T synonymous_variant 0.2
clpC1 4040552 c.153G>T synonymous_variant 0.22
embC 4240255 c.393G>A synonymous_variant 0.2
embC 4240582 c.720C>G synonymous_variant 0.25
embC 4240700 p.Val280Met missense_variant 0.5
embC 4241118 c.1257_1258insGGCAGC conservative_inframe_insertion 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244500 p.Pro423Arg missense_variant 0.29
embB 4245638 c.-876C>A upstream_gene_variant 0.67
embA 4246408 p.Gln1059Pro missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.79
embB 4246556 p.Ala15Pro missense_variant 0.79
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.8
embB 4246708 c.195C>T synonymous_variant 0.15
embB 4247518 p.Asn335Lys missense_variant 0.2
aftB 4266994 p.Leu615Ile missense_variant 0.29
aftB 4268240 p.Met199Ile missense_variant 0.22
aftB 4268891 c.-55G>T upstream_gene_variant 0.29
ubiA 4269467 p.Asn123His missense_variant 0.25
aftB 4269471 c.-635C>G upstream_gene_variant 0.22
ethA 4326626 p.Gly283Val missense_variant 0.4
ethA 4326693 p.Arg261Trp missense_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethR 4327087 c.-462G>C upstream_gene_variant 0.29
ethA 4328350 c.-877C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0