TB-Profiler result

Run: ERR2229655
Summary

Run ID: ERR2229655

Sample name:

Date: 31-03-2023 17:23:49

Number of reads: 506608

Percentage reads mapped: 99.15

Strain: lineage4.8

Drug-resistance: Other

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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
embC 4240748 p.Tyr296His missense_variant 0.12 ethambutol
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 7068 p.Tyr610Phe missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8500 p.Ala400Glu missense_variant 0.18
gyrA 9710 p.Leu803Phe missense_variant 0.12
mshA 575893 c.546C>T synonymous_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620608 p.Phe240Leu missense_variant 0.12
rpoB 761869 p.Asp688Val missense_variant 0.12
rpoB 761903 c.2097T>C synonymous_variant 0.12
rpoB 762029 c.2223C>G synonymous_variant 0.15
rpoB 762691 p.Pro962Leu missense_variant 0.25
rpoB 762852 p.Pro1016Thr missense_variant 0.18
rpoC 764914 p.Met515Ile missense_variant 0.13
rpoC 765863 p.Ile832Leu missense_variant 0.22
rpoC 766673 p.Gly1102Ser missense_variant 0.22
rpoC 767253 p.Pro1295Gln missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777179 c.1302G>A synonymous_variant 0.2
mmpL5 777767 c.714C>T synonymous_variant 0.18
mmpR5 779366 p.Gly126Val missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801391 p.Lys195* stop_gained 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417130 p.His73Leu missense_variant 0.12
atpE 1461208 p.Ile55Asn missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.13
rrl 1473789 n.132G>A non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674808 p.Val203Ile missense_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169596 p.Phe339Trp missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170412 c.201G>C synonymous_variant 0.13
PPE35 2170415 c.198A>G synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518759 c.645C>A synonymous_variant 0.18
folC 2747465 p.Pro45Leu missense_variant 0.17
ribD 2987365 p.Ala176Glu missense_variant 0.15
thyX 3068153 c.-208G>A upstream_gene_variant 0.11
thyA 3073848 c.624C>A synonymous_variant 0.12
ald 3086839 p.Thr7Ile missense_variant 0.11
ald 3087359 c.540C>T synonymous_variant 0.14
fbiD 3339324 c.207G>C synonymous_variant 0.13
Rv3083 3448356 c.-148G>A upstream_gene_variant 0.13
whiB7 3568633 p.Pro16Arg missense_variant 0.15
Rv3236c 3613192 c.-76G>C upstream_gene_variant 0.12
fbiB 3642710 c.1176G>T synonymous_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.29
rpoA 3877529 p.Thr327Ser missense_variant 0.12
rpoA 3877790 p.Glu240* stop_gained 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4247033 p.Ser174Arg missense_variant 0.33
embB 4247041 p.Phe176Leu missense_variant 0.4
ethA 4326476 p.Leu333Pro missense_variant 0.12
ethR 4327735 p.Phe63Leu missense_variant 0.25
ethA 4327749 c.-276G>T 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