TB-Profiler result

Run: ERR2229289
Summary

Run ID: ERR2229289

Sample name:

Date: 31-03-2023 16:57:16

Number of reads: 1218129

Percentage reads mapped: 99.12

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 576108 p.Ala254Gly missense_variant 0.33
mshA 576398 p.Tyr351Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775814 c.2667C>G synonymous_variant 0.2
mmpL5 775817 c.2664T>C synonymous_variant 0.2
mmpL5 775820 c.2661G>A synonymous_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.27
mmpL5 777122 c.1359C>T synonymous_variant 0.27
mmpL5 777128 c.1353A>G synonymous_variant 0.29
mmpL5 779094 c.-614C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169725 c.888T>C synonymous_variant 0.16
PPE35 2169902 c.711G>C synonymous_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518805 p.Asp231Asn missense_variant 0.12
kasA 2518809 p.Lys232Arg missense_variant 0.12
eis 2714223 c.1110C>A synonymous_variant 0.2
folC 2746281 p.Ile440Val missense_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612568 c.549G>C synonymous_variant 0.13
fbiB 3642379 p.Glu282Val missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039709 c.996C>T synonymous_variant 0.17
panD 4044280 c.2T>A start_lost 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244308 p.Val359Gly missense_variant 0.25
embA 4244714 c.1482C>A synonymous_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