TB-Profiler result

Run: ERR2229697
Summary

Run ID: ERR2229697

Sample name:

Date: 31-03-2023 17:27:45

Number of reads: 1207623

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
gyrA 7946 c.645C>A synonymous_variant 0.18
gyrA 8293 p.Leu331Pro missense_variant 0.1
mshA 575171 c.-177C>G upstream_gene_variant 0.2
mshA 575675 p.Arg110Ser missense_variant 0.13
ccsA 620454 c.564C>A synonymous_variant 0.12
rpoB 761741 c.1935G>A synonymous_variant 0.14
rpoB 762744 p.Gln980* stop_gained 0.13
rpoC 764341 c.972G>T synonymous_variant 0.12
rpoC 764584 c.1215G>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 p.Leu821Pro missense_variant 0.14
mmpL5 776021 c.2460G>C synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304048 p.Ala373Asp missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473196 n.1351C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474481 n.824G>A non_coding_transcript_exon_variant 0.12
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.13
rrl 1475288 n.1631G>A non_coding_transcript_exon_variant 0.15
inhA 1674555 p.Lys118Asn missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.654G>C synonymous_variant 0.11
katG 2154601 p.Gly504Val missense_variant 0.11
katG 2154836 p.Tyr426His missense_variant 0.1
katG 2155778 p.Thr112Ser missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289714 c.-473G>A upstream_gene_variant 0.14
kasA 2518606 c.492G>C synonymous_variant 0.12
kasA 2518609 p.Met165Ile missense_variant 0.14
eis 2715509 c.-177G>T upstream_gene_variant 0.14
ahpC 2726546 c.354C>G synonymous_variant 0.18
folC 2746425 p.Ala392Ser missense_variant 0.4
folC 2747587 c.12G>A synonymous_variant 0.12
Rv2752c 3064708 p.Arg495Leu missense_variant 0.12
Rv2752c 3066108 c.84C>T synonymous_variant 0.12
thyX 3067878 p.Val23Ala missense_variant 0.15
fprA 3474541 p.Ala179Pro missense_variant 0.11
fprA 3475256 p.Leu417Arg missense_variant 0.15
Rv3236c 3612222 p.Ala299Pro missense_variant 0.15
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
clpC1 4039031 c.1674T>C synonymous_variant 0.12
clpC1 4039498 p.Ile403Val missense_variant 0.15
panD 4044383 c.-102C>A upstream_gene_variant 0.14
embC 4240368 p.Val169Ala missense_variant 0.11
embC 4240689 p.Leu276Arg missense_variant 0.12
embC 4241550 p.Gly563Val missense_variant 0.14
embA 4242470 c.-763C>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243890 p.Gly220Trp missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.61
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.39
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4247027 p.Leu172Met missense_variant 0.17
embB 4247852 p.Thr447Ala missense_variant 0.11
ethA 4327424 p.Val17Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408105 p.Arg33Gln missense_variant 0.11