TB-Profiler result

Run: ERR2229199
Summary

Run ID: ERR2229199

Sample name:

Date: 31-03-2023 16:48:24

Number of reads: 775691

Percentage reads mapped: 99.06

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 5843 p.Lys202* stop_gained 0.29
gyrB 6770 p.Thr511Ala missense_variant 0.11
gyrB 7229 p.Thr664Ser missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.38
rpoC 764030 p.Asp221His missense_variant 0.17
rpoC 765671 p.Asp768Tyr missense_variant 0.33
rpoC 766087 c.2718C>G synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777453 p.Met343Thr missense_variant 0.12
mmpL5 778450 p.Gly11Cys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304957 p.Val676Asp missense_variant 0.29
embR 1417416 c.-69G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473842 n.185C>T non_coding_transcript_exon_variant 0.17
rrl 1473843 n.186G>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475855 n.2198A>T non_coding_transcript_exon_variant 0.15
rrl 1476120 n.2463A>G non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918129 p.Ser64Pro missense_variant 0.13
ndh 2103226 c.-184C>A upstream_gene_variant 0.2
PPE35 2167842 p.Pro924Arg missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2221982 p.Ala395Ser missense_variant 0.18
Rv1979c 2222681 p.Ala162Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288914 p.Asp110Tyr missense_variant 0.12
pncA 2290090 c.-849C>A upstream_gene_variant 0.14
kasA 2518035 c.-80C>A upstream_gene_variant 0.13
kasA 2519128 c.1014G>C synonymous_variant 0.5
kasA 2519131 c.1017G>C synonymous_variant 0.5
kasA 2519140 c.1026G>C synonymous_variant 0.5
kasA 2519143 c.1029G>C synonymous_variant 0.5
eis 2715435 c.-103C>T upstream_gene_variant 0.12
folC 2746157 p.Leu481Ser missense_variant 0.14
Rv2752c 3064723 p.Pro490Arg missense_variant 0.29
Rv2752c 3064865 p.Pro443Thr missense_variant 0.22
thyX 3068109 c.-164T>A upstream_gene_variant 0.2
thyA 3074140 p.Gln111Leu missense_variant 0.18
ald 3087626 c.809_813dupACCAG frameshift_variant 0.18
Rv3083 3448377 c.-126delC upstream_gene_variant 0.18
fprA 3474323 p.Ala106Val missense_variant 0.2
fprA 3475355 p.Leu450Arg missense_variant 0.29
Rv3236c 3612251 c.865delT frameshift_variant 0.15
fbiA 3640492 c.-51G>T upstream_gene_variant 0.33
fbiA 3641462 p.Pro307Leu missense_variant 0.17
fbiB 3642856 p.Ala441Asp missense_variant 0.38
clpC1 4038421 p.Arg762Ser missense_variant 0.17
clpC1 4038659 c.2046C>A synonymous_variant 0.18
clpC1 4039558 c.1146delC frameshift_variant 0.15
clpC1 4039632 p.Ile358Thr missense_variant 0.13
clpC1 4039682 c.1023C>T synonymous_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040028 p.Val226Ala missense_variant 0.25
embC 4241770 p.Ser636Arg missense_variant 0.17
embC 4242624 p.Gly921Val missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243420 p.Val63Glu missense_variant 0.18
embA 4243976 p.Phe248Leu missense_variant 0.15
embA 4244184 p.Ser318Leu missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4248697 c.2184A>T synonymous_variant 0.33
embB 4248972 p.Lys820Met missense_variant 0.4
aftB 4267219 p.Asp540Asn missense_variant 0.15
aftB 4268195 c.642G>A synonymous_variant 0.13
ethA 4327388 p.Thr29Ser missense_variant 0.22
ethR 4328092 p.Thr182Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408176 c.27T>C synonymous_variant 0.18
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0