TB-Profiler result

Run: ERR2229338
Summary

Run ID: ERR2229338

Sample name:

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

Number of reads: 1041210

Percentage reads mapped: 98.55

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
gyrB 6172 c.933C>T synonymous_variant 0.15
gyrB 6206 p.Ala323Ser missense_variant 0.13
gyrA 6580 c.-722C>A upstream_gene_variant 0.18
gyrB 6635 p.Ser466Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575440 c.93C>A synonymous_variant 0.14
mshA 576438 p.Ala364Gly missense_variant 0.11
mshA 576482 p.Val379Leu missense_variant 0.25
ccsA 620163 c.273G>A synonymous_variant 0.15
rpoC 764038 p.Trp223* stop_gained 0.14
rpoC 764050 c.681C>T synonymous_variant 0.15
rpoC 764715 p.Leu449Pro missense_variant 0.15
rpoC 765963 p.Leu865Ser missense_variant 0.12
mmpL5 775607 c.2874A>G synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775659 c.2821delC frameshift_variant 0.13
mmpL5 775871 c.2610C>T synonymous_variant 0.22
mmpL5 775874 c.2607C>A synonymous_variant 0.22
mmpS5 778790 p.Val39Ala missense_variant 0.12
mmpR5 779371 c.386delC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303304 p.Pro125Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305010 p.Val694Met missense_variant 0.13
Rv1258c 1406929 p.Ser138Pro missense_variant 0.11
embR 1417139 p.Ala70Glu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473950 n.293G>T non_coding_transcript_exon_variant 0.16
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474563 n.906G>C non_coding_transcript_exon_variant 0.29
rrl 1474667 n.1010G>C non_coding_transcript_exon_variant 0.22
rrl 1475139 n.1483delT non_coding_transcript_exon_variant 0.18
rrl 1476323 n.2666G>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.32
fabG1 1673349 c.-91G>C upstream_gene_variant 0.32
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.44
fabG1 1673566 p.Ala43Pro missense_variant 0.17
rpsA 1833927 p.Thr129Lys missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102909 p.Arg45Leu missense_variant 0.18
katG 2155892 p.Asp74Asn missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168798 c.1815T>C synonymous_variant 0.11
PPE35 2169308 c.1305C>T synonymous_variant 0.14
PPE35 2169323 c.1290C>G synonymous_variant 0.13
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2222612 p.Ile185Val missense_variant 0.13
Rv1979c 2222863 p.Thr101Ile missense_variant 0.18
Rv1979c 2223108 c.57C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518609 p.Met165Ile missense_variant 0.12
kasA 2518899 c.787delG frameshift_variant 0.14
ahpC 2726200 p.Leu3Pro missense_variant 0.11
folC 2747436 p.Asp55Tyr missense_variant 0.13
folC 2747747 c.-149C>T upstream_gene_variant 0.17
pepQ 2860047 c.372A>C synonymous_variant 0.29
thyX 3067340 c.606G>A synonymous_variant 0.2
ald 3087879 c.1060C>A synonymous_variant 0.13
fbiA 3640352 c.-191G>C upstream_gene_variant 0.13
fbiA 3641191 p.Val217Leu missense_variant 0.15
fbiB 3642495 p.Leu321Phe missense_variant 0.12
alr 3840730 p.Val231Leu missense_variant 0.15
rpoA 3877823 p.Ala229Thr missense_variant 0.17
ddn 3987007 p.Lys55Met missense_variant 0.18
clpC1 4038336 p.Leu790Pro missense_variant 0.12
clpC1 4038740 c.1965G>C synonymous_variant 0.14
clpC1 4039018 p.Ser563Ala missense_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.15
clpC1 4039031 c.1674T>C synonymous_variant 0.12
clpC1 4040411 c.294T>G synonymous_variant 0.13
clpC1 4040415 p.Gln97Arg missense_variant 0.14
clpC1 4040417 c.288G>T synonymous_variant 0.13
clpC1 4040556 p.Glu50Val missense_variant 0.13
embC 4240355 p.Ala165Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243897 p.Ala222Val missense_variant 0.2
embA 4244082 p.Ala284Thr missense_variant 0.12
embB 4246110 c.-404C>A upstream_gene_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.8
embB 4246555 c.42G>C synonymous_variant 0.78
embB 4246556 p.Ala15Pro missense_variant 0.78
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4246748 p.Phe79Leu missense_variant 0.25
ethR 4326597 c.-952A>G upstream_gene_variant 0.13
ethA 4326830 p.Gln215Arg missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0