TB-Profiler result

Run: ERR3994124
Summary

Run ID: ERR3994124

Sample name:

Date: 01-04-2023 03:42:59

Number of reads: 782793

Percentage reads mapped: 99.95

Strain: lineage4.3.4

Drug-resistance: Other

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.15
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
rpsL 781585 p.Arg9His missense_variant 1.0 streptomycin
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 5084 c.-156G>A upstream_gene_variant 1.0
gyrB 6780 p.His514Leu missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491549 p.Ala256Asp missense_variant 0.29
mshA 575342 c.-6G>A upstream_gene_variant 0.67
ccsA 619822 c.-69G>T upstream_gene_variant 1.0
rpoB 760022 c.216T>C synonymous_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766194 p.Gln942Arg missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776450 c.2031C>T synonymous_variant 0.29
mmpL5 777352 c.1129C>A synonymous_variant 0.18
mmpL5 777909 p.Ala191Gly missense_variant 0.29
mmpL5 778501 c.-21C>T upstream_gene_variant 0.2
rplC 801145 p.Asp113Asn missense_variant 0.67
Rv1258c 1406325 p.Arg339Leu missense_variant 0.5
embR 1417325 p.Glu8Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrl 1474076 n.419C>T non_coding_transcript_exon_variant 0.25
rrl 1474606 n.949A>G non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
inhA 1674962 p.Thr254Met missense_variant 0.5
rpsA 1834296 p.Val252Ala missense_variant 0.67
tlyA 1918515 c.576C>T synonymous_variant 0.2
ndh 2102600 p.Arg148His missense_variant 0.2
katG 2156247 c.-136T>C upstream_gene_variant 0.4
katG 2156369 c.-258C>T upstream_gene_variant 0.5
Rv1979c 2222703 c.462C>T synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518482 p.Val123Ala missense_variant 1.0
eis 2714506 p.Pro276Leu missense_variant 0.4
folC 2747780 c.-182C>T upstream_gene_variant 0.5
pepQ 2859703 c.714_715dupGT frameshift_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 0.4
Rv3236c 3612359 p.Gly253Glu missense_variant 1.0
fbiA 3640950 p.Trp136* stop_gained 0.33
fbiA 3641330 p.Ile263Asn missense_variant 0.5
alr 3840824 p.Tyr199* stop_gained 0.18
alr 3841513 c.-93A>T upstream_gene_variant 0.17
clpC1 4039991 c.714G>A synonymous_variant 1.0
embC 4241285 p.Pro475Thr missense_variant 1.0
aftB 4267052 c.1785C>T synonymous_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338612 c.-91C>G upstream_gene_variant 0.29
gid 4407663 c.540A>T synonymous_variant 0.4
gid 4408156 p.Leu16Arg missense_variant 1.0