TB-Profiler result

Run: ERR2229741
Summary

Run ID: ERR2229741

Sample name:

Date: 31-03-2023 17:30:39

Number of reads: 578050

Percentage reads mapped: 99.38

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 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
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
rpoB 760570 p.Thr255Arg missense_variant 0.2
rpoB 761024 c.1218C>T synonymous_variant 0.14
rpoC 763619 p.Arg84Ser missense_variant 0.25
rpoC 764777 p.Lys470Glu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>C synonymous_variant 0.25
mmpL5 775718 c.2763C>G synonymous_variant 0.25
mmpL5 775723 p.Ile920Val missense_variant 0.25
mmpL5 775724 c.2757G>C synonymous_variant 0.25
mmpL5 775850 p.Ser877Arg missense_variant 0.22
mmpL5 776018 c.2463G>C synonymous_variant 0.22
mmpL5 776021 c.2460G>C synonymous_variant 0.22
mmpL5 777119 p.His454Gln missense_variant 0.12
mmpL5 777122 c.1359C>T synonymous_variant 0.12
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 777136 p.Met449Leu missense_variant 0.13
mmpR5 778142 c.-848G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800953 p.Ala49Pro missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475016 n.1359C>A non_coding_transcript_exon_variant 0.15
rrl 1475420 n.1763G>A non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
inhA 1673613 c.-589C>A upstream_gene_variant 0.17
fabG1 1673740 p.Thr101Ala missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102135 p.Val303Asp missense_variant 0.17
ndh 2102146 c.897G>C synonymous_variant 0.22
katG 2154974 p.Thr380Ala missense_variant 0.15
katG 2155320 c.792G>A synonymous_variant 0.18
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170232 c.381T>C synonymous_variant 0.14
PPE35 2170235 c.378T>C synonymous_variant 0.13
PPE35 2170238 c.375T>G synonymous_variant 0.14
PPE35 2170244 c.369G>A synonymous_variant 0.14
Rv1979c 2222481 c.684G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066024 c.168T>C synonymous_variant 0.15
thyX 3067340 c.606G>A synonymous_variant 0.22
thyA 3074167 p.Pro102Leu missense_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612381 c.736C>T synonymous_variant 0.17
Rv3236c 3612744 p.Thr125Ala missense_variant 0.25
Rv3236c 3612860 p.Leu86Pro missense_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4040057 c.648C>T synonymous_variant 0.18
clpC1 4040768 c.-64G>T upstream_gene_variant 0.29
clpC1 4040819 c.-115G>C upstream_gene_variant 0.15
embC 4240654 c.792C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243713 p.Thr161Ser missense_variant 0.15
embB 4247293 c.780G>A synonymous_variant 0.2
embB 4247855 p.Gly448Arg missense_variant 0.25
embB 4248489 p.Ala659Glu missense_variant 0.33
embB 4248749 p.Gly746Ser missense_variant 0.14
aftB 4267251 p.Asp529Gly missense_variant 0.2
ubiA 4269911 c.-78G>T upstream_gene_variant 0.12
ethA 4326225 p.Val417Leu missense_variant 0.12
whiB6 4338349 p.Arg58Pro missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0