TB-Profiler result

Run: ERR2229064
Summary

Run ID: ERR2229064

Sample name:

Date: 31-03-2023 16:34:46

Number of reads: 970299

Percentage reads mapped: 99.51

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
mshA 576108 p.Ala254Gly missense_variant 0.3
ccsA 619842 c.-49G>T upstream_gene_variant 0.12
rpoC 764541 p.Val391Gly missense_variant 0.12
rpoC 764543 p.Thr392Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777561 c.919delG frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473367 n.1522G>A non_coding_transcript_exon_variant 0.13
rrs 1473375 n.1530T>C non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476083 n.2426T>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
rpsA 1834983 p.Ala481Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102829 p.Thr72Ser missense_variant 0.12
PPE35 2167815 p.Tyr933Phe missense_variant 0.14
PPE35 2167885 p.Gly910Ser missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987347 p.Pro170Leu missense_variant 0.13
ribD 2987488 p.Pro217His missense_variant 0.12
thyX 3067534 p.Ala138Pro missense_variant 0.18
thyX 3067603 c.343C>A synonymous_variant 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474230 p.Arg75Leu missense_variant 0.12
Rv3236c 3611973 p.Val382Leu missense_variant 0.11
Rv3236c 3612506 p.His204Arg missense_variant 0.12
fbiB 3640782 c.-753C>G upstream_gene_variant 0.12
alr 3840778 c.642delG frameshift_variant 0.11
alr 3840828 p.Val198Asp missense_variant 0.14
embC 4240562 p.Met234Leu missense_variant 0.14
embC 4241967 p.Gly702Val missense_variant 0.17
embA 4242442 c.-791G>T upstream_gene_variant 0.15
embC 4242453 c.2592delG frameshift_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269183 c.-347T>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408429 c.-227A>C upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0