TB-Profiler result

Run: ERR2229430
Summary

Run ID: ERR2229430

Sample name:

Date: 31-03-2023 17:11:45

Number of reads: 1407630

Percentage reads mapped: 99.18

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 491342 p.Arg187Leu missense_variant 0.12
mshA 576114 p.Arg256Pro missense_variant 0.22
ccsA 619733 c.-158G>T upstream_gene_variant 0.15
rpoC 766162 p.Asp931Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 0.21
inhA 1674738 c.539delG frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.654G>C synonymous_variant 0.12
ndh 2102392 c.651C>A synonymous_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.16
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.46
PPE35 2170147 p.Ser156Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746594 c.1005T>C synonymous_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.17
fprA 3475021 p.Gly339Trp missense_variant 0.12
Rv3236c 3612877 c.240C>T synonymous_variant 0.12
fbiB 3642227 c.693A>G synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.24
clpC1 4039031 c.1674T>C synonymous_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039714 p.Tyr331His missense_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.19
panD 4043999 p.Asp95Asn missense_variant 0.14
embC 4241123 p.Arg421Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243589 c.357C>T synonymous_variant 0.17
embA 4244747 c.1515T>C synonymous_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.14
aftB 4268135 c.702G>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0