TB-Profiler result

Run: ERR2229095
Summary

Run ID: ERR2229095

Sample name:

Date: 31-03-2023 16:38:14

Number of reads: 535084

Percentage reads mapped: 99.37

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 490892 p.Val37Ala missense_variant 0.12
mshA 575409 p.Gly21Val missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 762474 p.Gly890Cys missense_variant 0.13
rpoB 762856 p.Val1017Asp missense_variant 0.18
rpoC 763220 c.-150G>C upstream_gene_variant 0.11
rpoB 763222 p.Ile1139Thr missense_variant 0.11
rpoC 765525 p.Ala719Val missense_variant 0.22
rpoC 767002 c.3633G>T synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776179 c.2302T>C synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416506 p.Thr281Ile missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.23
fabG1 1673359 c.-81T>C upstream_gene_variant 0.23
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23
fabG1 1673380 c.-60C>G upstream_gene_variant 0.45
inhA 1673791 c.-411C>A upstream_gene_variant 0.25
rpsA 1834641 p.Glu367Val missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101680 p.Ser455Pro missense_variant 0.11
ndh 2102327 p.Leu239Pro missense_variant 0.29
ndh 2102373 p.Met224Leu missense_variant 0.4
ndh 2102460 p.His195Asp missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170147 p.Ser156Ala missense_variant 0.11
Rv1979c 2221997 p.Pro390Ser missense_variant 0.15
Rv1979c 2222478 p.Leu229Phe missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289177 p.Thr22Asn missense_variant 0.25
kasA 2518491 p.Tyr126Cys missense_variant 0.15
thyX 3067340 c.606G>A synonymous_variant 0.27
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612086 p.Ala344Val missense_variant 0.11
fbiA 3640354 c.-189C>A upstream_gene_variant 0.13
fbiB 3642096 p.Val188Met missense_variant 0.22
rpoA 3878049 c.459G>T synonymous_variant 0.33
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
ddn 3987252 c.410delA frameshift_variant 0.11
clpC1 4038748 p.Arg653Gly missense_variant 0.12
embC 4241896 c.2036delT frameshift_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.33
embB 4246837 p.Asp108Glu missense_variant 0.22
embB 4247438 p.Val309Phe missense_variant 0.17
embB 4247976 p.Val488Ala missense_variant 0.11
embB 4249361 p.Ala950Thr missense_variant 0.17
aftB 4267895 p.Phe314Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0