TB-Profiler result

Run: ERR2228833
Summary

Run ID: ERR2228833

Sample name:

Date: 31-03-2023 16:22:23

Number of reads: 970146

Percentage reads mapped: 99.32

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 0.98
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
mshA 576699 p.Glu451Ala missense_variant 0.22
ccsA 619787 c.-104T>G upstream_gene_variant 0.15
rpoB 759671 c.-136G>T upstream_gene_variant 0.18
rpoC 763560 p.Lys64Met missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.27
mmpS5 778623 p.Thr95Pro missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303982 p.Val351Gly missense_variant 0.29
fbiC 1304897 p.Leu656Arg missense_variant 0.25
fbiC 1304981 p.Lys684Met missense_variant 0.22
Rv1258c 1406284 p.Thr353Pro missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474013 n.356A>T non_coding_transcript_exon_variant 0.3
rrl 1476008 n.2351A>T non_coding_transcript_exon_variant 0.67
rrl 1476016 n.2359T>A non_coding_transcript_exon_variant 1.0
inhA 1674421 p.Leu74Val missense_variant 0.25
inhA 1674752 p.Val184Gly missense_variant 0.13
rpsA 1834941 p.Asp467Ala missense_variant 0.22
tlyA 1917817 c.-123A>C upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102018 p.Tyr342Cys missense_variant 0.14
ndh 2103230 c.-188T>G upstream_gene_variant 0.21
katG 2155525 p.Val196Gly missense_variant 0.3
katG 2155549 p.Val188Gly missense_variant 0.33
katG 2155558 p.Phe185Cys missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168012 c.2601C>G synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.2
PPE35 2169049 p.Ile522Phe missense_variant 0.22
PPE35 2169662 c.951T>A synonymous_variant 0.25
PPE35 2169683 c.930C>A synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519224 c.1110C>A synonymous_variant 0.12
eis 2715073 p.Val87Pro missense_variant 0.2
ahpC 2726509 p.Leu106* stop_gained 0.29
folC 2746634 p.Asp322Ala missense_variant 0.31
folC 2747389 c.210G>A synonymous_variant 0.18
Rv2752c 3065692 p.His167Pro missense_variant 0.17
thyX 3067329 p.Val206Ala missense_variant 0.25
thyX 3067338 p.His203Pro missense_variant 0.22
thyA 3074341 p.Leu44Gln missense_variant 0.2
thyA 3074348 p.Phe42Ile missense_variant 0.2
thyA 3074349 c.123T>G synonymous_variant 0.22
thyA 3074417 p.Ser19Thr missense_variant 0.23
ald 3087867 p.Leu350Val missense_variant 0.19
fbiD 3339711 c.594A>C synonymous_variant 0.28
fprA 3474248 p.Asn81Ile missense_variant 0.26
fprA 3474634 p.Leu210Val missense_variant 0.17
fprA 3474884 p.Glu293Ala missense_variant 0.13
fprA 3474951 c.945T>G synonymous_variant 0.17
fprA 3475331 p.Val442Gly missense_variant 0.21
alr 3841539 c.-119C>T upstream_gene_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4038961 p.Met582Leu missense_variant 0.25
clpC1 4038996 p.Leu570* stop_gained 0.22
clpC1 4040902 c.-198T>G upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245196 p.Ile655Asn missense_variant 0.25
embA 4245655 p.Asp808Ala missense_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4249728 p.Asp1072Ala missense_variant 0.18
aftB 4267763 c.1074C>A synonymous_variant 0.22
aftB 4267847 c.990C>G synonymous_variant 0.18
ethR 4327450 c.-99G>C upstream_gene_variant 0.2
ethR 4327625 p.Glu26Ala missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0