TB-Profiler result

Run: ERR2229600
Summary

Run ID: ERR2229600

Sample name:

Date: 31-03-2023 17:20:51

Number of reads: 628455

Percentage reads mapped: 99.11

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 5972 p.Lys245* stop_gained 0.2
gyrB 6364 p.Leu375Phe missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8501 c.1200G>A synonymous_variant 0.12
rpoB 760106 c.300G>A synonymous_variant 0.11
rpoB 760367 c.561G>A synonymous_variant 0.17
rpoB 760707 p.Asp301Asn missense_variant 0.14
rpoC 762572 c.-798C>A upstream_gene_variant 0.18
rpoC 763476 p.Tyr36Phe missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775962 p.Val840Gly missense_variant 0.22
mmpL5 776018 c.2463G>C synonymous_variant 0.17
mmpL5 776021 c.2460G>C synonymous_variant 0.13
mmpL5 776098 p.Thr795Ala missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781770 p.Gly71Cys missense_variant 0.17
rplC 800933 p.Pro42Leu missense_variant 0.22
rplC 801402 c.594T>C synonymous_variant 0.11
fbiC 1303517 p.Met196Lys missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303947 c.1019delG frameshift_variant 0.13
fbiC 1303979 p.Gly350Val missense_variant 0.14
fbiC 1304468 p.Glu513Val missense_variant 0.17
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.17
Rv1258c 1406946 p.Ala132Gly missense_variant 0.17
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.18
Rv1258c 1407462 c.-122A>G upstream_gene_variant 0.25
embR 1417261 c.87A>G synonymous_variant 0.12
embR 1417268 p.Pro27Arg missense_variant 0.12
atpE 1461261 p.Leu73Met missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834820 p.Met427Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.16
PPE35 2167967 c.2646A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.26
PPE35 2169272 c.1341C>G synonymous_variant 0.23
PPE35 2169278 c.1335T>C synonymous_variant 0.26
PPE35 2169281 c.1332T>G synonymous_variant 0.32
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170454 c.159C>G synonymous_variant 0.12
PPE35 2170457 c.156G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518112 c.-3C>T upstream_gene_variant 0.13
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2519128 c.1014G>C synonymous_variant 0.15
kasA 2519131 c.1017G>C synonymous_variant 0.15
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.16
eis 2715114 c.219T>C synonymous_variant 0.2
pepQ 2860474 c.-56C>A upstream_gene_variant 0.14
Rv2752c 3065162 p.Asn344Asp missense_variant 0.25
thyX 3067419 p.Pro176Arg missense_variant 0.29
thyA 3074252 p.Glu74* stop_gained 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.28
rpoA 3877936 p.Lys191Met missense_variant 0.15
clpC1 4039042 p.Ser555Thr missense_variant 0.15
clpC1 4039645 p.His354Asp missense_variant 0.18
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.19
clpC1 4040001 p.His235Ala missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.12
clpC1 4040319 p.Ala129Gly missense_variant 0.12
clpC1 4040535 c.169delG frameshift_variant 0.17
panD 4044143 p.Val47Ile missense_variant 0.18
embC 4241486 p.Leu542Met missense_variant 0.22
embC 4241617 p.Lys585Asn missense_variant 0.22
embC 4241783 p.Trp641Arg missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244175 p.Ala315Pro missense_variant 0.12
embA 4244184 p.Ser318Leu missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247310 p.Arg266His missense_variant 0.18
embB 4248939 p.Pro809Leu missense_variant 0.17
embB 4249531 c.3018C>A synonymous_variant 0.22
aftB 4268340 p.Pro166Leu missense_variant 0.17
aftB 4268701 p.Gly46Arg missense_variant 0.25
ethA 4326539 p.Val312Glu missense_variant 0.33
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0