TB-Profiler result

Run: ERR2652953
Summary

Run ID: ERR2652953

Sample name:

Date: 31-03-2023 22:25:01

Number of reads: 466745

Percentage reads mapped: 99.73

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 5794 c.555C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8259 p.Arg320Cys missense_variant 0.12
gyrA 8784 p.Arg495Ser missense_variant 0.2
mshA 575375 c.29delC frameshift_variant 0.15
mshA 576783 p.Gly479Asp missense_variant 0.14
ccsA 620741 p.Thr284Met missense_variant 0.17
rpoB 761632 p.Ala609Val missense_variant 0.18
rpoB 761791 p.Arg662His missense_variant 0.12
rpoB 761882 c.2078delG frameshift_variant 0.15
rpoC 763850 p.Ala161Thr missense_variant 0.12
rpoC 764081 c.715_716delAA frameshift_variant 0.17
rpoC 764481 p.Lys371Met missense_variant 0.11
rpoC 764712 p.Ala448Val missense_variant 0.18
rpoC 767240 p.Gln1291* stop_gained 0.25
mmpL5 777227 c.1254C>A synonymous_variant 0.11
mmpL5 777513 p.Cys323Tyr missense_variant 0.13
rplC 800956 p.Val50Met missense_variant 0.22
fbiC 1303643 p.Pro238Leu missense_variant 1.0
Rv1258c 1406925 p.Leu139Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473568 n.-90G>T upstream_gene_variant 0.11
rrl 1474758 n.1104delA non_coding_transcript_exon_variant 0.15
rrl 1474936 n.1279C>T non_coding_transcript_exon_variant 0.12
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.18
rpsA 1834344 p.Asp268Gly missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102873 p.Gln57Arg missense_variant 0.15
katG 2155005 c.1107C>T synonymous_variant 0.17
Rv1979c 2222681 p.Ala162Thr missense_variant 0.11
pncA 2289718 c.-477G>T upstream_gene_variant 0.22
kasA 2518757 p.Ala215Thr missense_variant 0.12
ahpC 2726129 c.-64G>A upstream_gene_variant 0.29
ahpC 2726677 p.Leu162Gln missense_variant 0.17
folC 2747493 p.Gln36* stop_gained 0.22
pepQ 2859311 p.Ala370Ser missense_variant 0.18
pepQ 2860566 c.-148C>A upstream_gene_variant 0.2
Rv2752c 3065418 c.774A>G synonymous_variant 0.29
Rv2752c 3065975 p.Asp73Asn missense_variant 0.11
thyX 3067264 p.Ala228Thr missense_variant 0.2
ald 3087223 p.Glu135Gly missense_variant 0.22
fbiD 3339182 p.Ala22Val missense_variant 0.13
fbiD 3339525 c.408G>T synonymous_variant 0.22
Rv3083 3449279 p.Arg259Pro missense_variant 0.12
Rv3236c 3611999 p.Thr373Ile missense_variant 0.2
Rv3236c 3612424 c.693G>T synonymous_variant 0.17
rpoA 3877848 c.660C>T synonymous_variant 0.15
clpC1 4038276 p.Glu810Gly missense_variant 0.12
panD 4044238 p.Val15Ala missense_variant 0.29
embC 4239863 c.1A>G start_lost 0.12
embC 4240835 p.Gly325Cys missense_variant 0.29
embC 4240860 p.Leu333Arg missense_variant 1.0
embC 4242620 p.Val920Ile missense_variant 0.12
embA 4243882 p.Ala217Val missense_variant 0.12
embB 4246103 c.-411C>T upstream_gene_variant 0.15
embB 4248323 p.Ala604Thr missense_variant 0.18
aftB 4268268 p.Ala190Val missense_variant 0.13
ethA 4326866 p.Thr203Met missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407765 c.438G>T synonymous_variant 0.22