TB-Profiler result

Run: ERR1950061
Summary

Run ID: ERR1950061

Sample name:

Date: 31-03-2023 15:38:50

Number of reads: 529935

Percentage reads mapped: 99.57

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 5149 c.-91G>A upstream_gene_variant 0.11
gyrB 6120 p.Asn294Ser missense_variant 0.12
gyrB 6359 p.Lys374Glu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7544 p.Met81Ile missense_variant 0.15
gyrA 9677 c.2376C>T synonymous_variant 0.12
gyrA 9807 p.Thr836Ala missense_variant 0.13
mshA 575465 p.Ala40Thr missense_variant 0.13
mshA 576279 p.Gly311Val missense_variant 0.22
rpoC 763607 p.Val80Ile missense_variant 0.11
rpoC 765459 p.Ile697Thr missense_variant 0.11
rpoC 766881 p.Gly1171Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.15
mmpL5 776081 c.2400G>A synonymous_variant 0.15
mmpL5 776087 c.2394C>G synonymous_variant 0.15
mmpL5 776093 c.2386_2388delCGCinsAGA synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 0.14
mmpL5 776103 p.Ile793Gly missense_variant 0.15
mmpL5 776105 c.2376G>C synonymous_variant 0.13
mmpL5 777704 c.777G>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304457 p.Cys509* stop_gained 0.29
Rv1258c 1406092 p.Ser417Thr missense_variant 0.14
embR 1416255 p.Asp365Asn missense_variant 0.11
embR 1416647 c.700delA frameshift_variant 0.1
embR 1417390 c.-43A>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673347 c.-93C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102544 p.Arg167Trp missense_variant 0.12
ndh 2102836 c.207T>A synonymous_variant 0.11
katG 2154103 p.Pro670Arg missense_variant 0.11
katG 2154305 p.Pro603Thr missense_variant 0.15
PPE35 2168047 p.Leu856Val missense_variant 0.11
PPE35 2168051 p.Val854Ile missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169520 p.Gly365Ser missense_variant 0.14
PPE35 2169827 c.786G>A synonymous_variant 0.18
PPE35 2170395 p.Ala73Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290040 c.-799A>C upstream_gene_variant 0.29
eis 2714265 c.1068G>A synonymous_variant 0.13
pepQ 2860024 p.Arg132His missense_variant 0.18
Rv3083 3448396 c.-108T>C upstream_gene_variant 0.14
fprA 3474627 p.Phe207Leu missense_variant 0.18
Rv3236c 3612007 c.1110C>A synonymous_variant 0.14
Rv3236c 3612154 c.963T>C synonymous_variant 0.4
fbiB 3642011 c.477C>A synonymous_variant 0.14
alr 3840305 c.1116T>C synonymous_variant 0.15
alr 3841223 c.198G>A synonymous_variant 0.11
rpoA 3877602 p.His302Gln missense_variant 0.13
rpoA 3877907 p.Ser201Pro missense_variant 0.2
ddn 3986790 c.-54G>A upstream_gene_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.1
clpC1 4040182 p.Gly175Ser missense_variant 0.12
panD 4044046 p.Val79Ala missense_variant 0.12
panD 4044195 c.87T>C synonymous_variant 0.13
embC 4240200 p.Ala113Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243897 p.Ala222Val missense_variant 0.33
embA 4244536 p.Gly435Val missense_variant 0.4
embB 4247470 c.957T>C synonymous_variant 0.11
ethA 4327680 c.-207A>G upstream_gene_variant 0.12
ethA 4328272 c.-799C>T upstream_gene_variant 0.12
whiB6 4338205 p.Val106Ala 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