TB-Profiler result

Run: ERR2229381
Summary

Run ID: ERR2229381

Sample name:

Date: 31-03-2023 17:07:53

Number of reads: 1105788

Percentage reads mapped: 98.92

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575731 c.385delC frameshift_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576111 p.Ala255Gly missense_variant 0.29
rpoB 759669 c.-138G>A upstream_gene_variant 0.15
rpoB 760995 p.Arg397Trp missense_variant 0.15
rpoB 761767 p.Val654Ala missense_variant 0.13
rpoC 763850 p.Ala161Ser missense_variant 0.18
rpoC 764111 p.Tyr248His missense_variant 0.11
rpoC 764426 c.1057C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.13
mmpL5 776021 c.2460G>C synonymous_variant 0.13
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 777157 c.1324C>A synonymous_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.13
mmpL5 777526 p.Gly319Cys missense_variant 0.13
mmpL5 778600 c.-120C>T upstream_gene_variant 0.14
mmpS5 778653 p.Ala85Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303379 p.Arg150Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303868 p.Asp313Val missense_variant 0.13
fbiC 1304831 p.Ser634Tyr missense_variant 0.12
Rv1258c 1406561 c.780G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473285 n.1443dupC non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475440 n.1783T>C non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
fabG1 1674074 p.Gly212Asp missense_variant 0.17
inhA 1674221 p.Gly7Ala missense_variant 0.11
inhA 1674789 c.588G>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102727 p.His106Tyr missense_variant 0.17
ndh 2102780 p.Asn88Thr missense_variant 0.17
katG 2155197 c.915C>T synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.37
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.23
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169602 c.1011C>A synonymous_variant 0.16
PPE35 2169890 c.723C>T synonymous_variant 0.15
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.26
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.64
PPE35 2170189 p.Glu142Gln missense_variant 0.15
Rv1979c 2222324 p.Lys281Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.13
kasA 2518882 c.768C>A synonymous_variant 0.13
kasA 2519140 c.1026G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.15
eis 2715575 c.-243G>T upstream_gene_variant 0.14
ahpC 2725946 c.-247A>G upstream_gene_variant 0.13
ahpC 2726624 c.432C>A synonymous_variant 0.12
folC 2746376 p.Ser408* stop_gained 0.12
folC 2746412 p.Pro396Leu missense_variant 0.14
Rv2752c 3064864 p.Pro443Leu missense_variant 0.15
thyX 3067340 c.606G>A synonymous_variant 0.14
thyX 3067879 p.Val23Leu missense_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612992 p.Ser42* stop_gained 0.14
fbiB 3641573 p.Glu13Asp missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877775 p.Ala245Ser missense_variant 0.12
rpoA 3878533 c.-26G>T upstream_gene_variant 0.25
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4039498 p.Ile403Val missense_variant 0.17
clpC1 4039508 c.1197G>C synonymous_variant 0.15
clpC1 4039691 c.1014G>C synonymous_variant 0.15
embC 4240654 c.792C>T synonymous_variant 0.17
embC 4242092 c.2230T>C synonymous_variant 0.18
embA 4242478 c.-755C>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.32
embB 4246548 p.Pro12Gln missense_variant 0.41
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.6
aftB 4266979 p.Gly620Trp missense_variant 0.2
ethA 4326513 p.Thr321Ser missense_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407925 p.Pro93Leu missense_variant 0.12
gid 4408309 c.-107A>C upstream_gene_variant 0.14
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0