TB-Profiler result

Run: ERR2229005
Summary

Run ID: ERR2229005

Sample name:

Date: 31-03-2023 16:30:13

Number of reads: 748123

Percentage reads mapped: 99.5

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
fgd1 491436 c.654T>A synonymous_variant 0.15
rpoC 763671 p.Val101Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.14
mmpL5 776021 c.2460G>C synonymous_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.12
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
rrl 1474021 n.364A>T non_coding_transcript_exon_variant 0.18
rrl 1475175 n.1518G>T non_coding_transcript_exon_variant 0.12
rpsA 1834373 p.Ala278Ser missense_variant 0.11
rpsA 1834783 p.Trp414* stop_gained 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102913 p.Ala44Thr missense_variant 0.15
ndh 2102955 p.Ala30Thr missense_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.24
PPE35 2169272 c.1341C>G synonymous_variant 0.24
PPE35 2169278 c.1335T>C synonymous_variant 0.29
PPE35 2169281 c.1332T>G synonymous_variant 0.3
PPE35 2169902 c.711G>C synonymous_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519041 c.927C>T synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.19
kasA 2519143 c.1029G>C synonymous_variant 0.2
kasA 2519153 p.Ile347Val missense_variant 0.21
pepQ 2859605 p.Gly272Trp missense_variant 0.22
thyX 3067855 p.Gly31Cys missense_variant 0.17
fprA 3475028 p.Ile341Thr missense_variant 0.12
Rv3236c 3612132 p.Ala329Ser missense_variant 0.12
fbiA 3640687 p.Asp49Asn missense_variant 0.14
fbiB 3640956 c.-579G>C upstream_gene_variant 0.18
rpoA 3878403 c.105C>T synonymous_variant 0.12
clpC1 4038896 c.1809C>A synonymous_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4039708 p.Glu333Lys missense_variant 0.11
embC 4240379 p.Gln173* stop_gained 0.12
embC 4240843 c.981C>T synonymous_variant 0.12
embC 4240847 p.Asp329Asn missense_variant 0.12
embC 4241538 p.Gly559Asp missense_variant 1.0
embC 4242458 p.Ser866Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245587 c.-927G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0