TB-Profiler result

Run: ERR2229024
Summary

Run ID: ERR2229024

Sample name:

Date: 31-03-2023 16:30:48

Number of reads: 908372

Percentage reads mapped: 60.08

Strain: lineage4

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
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
gyrA 7369 p.Glu23Gly missense_variant 0.18
gyrA 8655 p.Ile452Val missense_variant 0.11
gyrA 8714 p.Lys471Asn missense_variant 0.29
gyrA 8784 p.Arg495Gly missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576435 p.Gln363Arg missense_variant 0.15
ccsA 620096 p.His69Pro missense_variant 0.2
ccsA 620426 p.Val179Gly missense_variant 0.29
ccsA 620692 p.Ser268Ala missense_variant 0.18
rpoB 759776 c.-31T>A upstream_gene_variant 0.29
rpoB 762057 p.Ile751Val missense_variant 0.12
rpoB 762062 c.2256T>C synonymous_variant 0.12
rpoB 762065 c.2259T>C synonymous_variant 0.12
rpoB 762083 c.2277T>C synonymous_variant 0.15
rpoB 762086 c.2280G>C synonymous_variant 0.18
rpoB 762101 c.2295C>G synonymous_variant 0.17
rpoB 762114 p.Ile770Val missense_variant 0.18
rpoB 763093 p.Val1096Gly missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.24
mmpL5 775995 p.Ile829Asn missense_variant 0.33
mmpL5 776493 p.Gln663Leu missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304998 p.Trp690Arg missense_variant 0.22
Rv1258c 1406099 c.1242C>A synonymous_variant 0.18
Rv1258c 1406992 p.Gly117Ser missense_variant 0.25
atpE 1461151 p.Ile36Asn missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472444 n.599A>T non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.1
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.11
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.13
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.13
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14
rrl 1475681 n.2024C>T non_coding_transcript_exon_variant 0.18
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.29
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.4
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.12
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
fabG1 1673560 p.Lys41Gln missense_variant 0.11
fabG1 1673861 p.Val141Gly missense_variant 0.27
fabG1 1674082 p.Ala215Pro missense_variant 0.11
inhA 1674764 p.Leu188Pro missense_variant 0.18
inhA 1674977 p.Tyr259Ser missense_variant 0.25
rpsA 1834486 p.Glu315Asp missense_variant 0.15
rpsA 1834543 c.1002C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154592 p.Val507Gly missense_variant 0.2
katG 2154866 p.Ile416Phe missense_variant 0.29
katG 2155614 c.498T>G synonymous_variant 0.22
katG 2156313 c.-202T>A upstream_gene_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169900 p.Gly238Val missense_variant 0.22
Rv1979c 2222275 p.Asn297Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289824 c.-584A>T upstream_gene_variant 0.38
kasA 2518035 c.-80C>A upstream_gene_variant 0.2
kasA 2518585 p.Gln157His missense_variant 0.2
folC 2746535 p.Asn355Ile missense_variant 0.29
folC 2746805 p.Val265Gly missense_variant 0.18
pepQ 2859629 p.Leu264Val missense_variant 0.29
pepQ 2860114 p.Val102Gly missense_variant 0.17
pepQ 2860159 p.Ala87Val missense_variant 0.18
ribD 2986831 c.-8T>C upstream_gene_variant 0.17
thyX 3067598 c.348C>A synonymous_variant 0.17
thyX 3067776 p.Asn57Thr missense_variant 0.43
thyX 3067928 c.18G>T synonymous_variant 0.18
ald 3087229 p.Ala137Asp missense_variant 0.14
fprA 3474281 p.Glu92Ala missense_variant 0.17
Rv3236c 3612572 p.Val182Gly missense_variant 0.22
Rv3236c 3613024 c.93G>A synonymous_variant 0.14
fbiA 3641135 p.Glu198Ala missense_variant 0.17
fbiB 3641511 c.-24G>T upstream_gene_variant 0.18
fbiA 3641512 p.Cys324Gly missense_variant 0.18
fbiB 3641624 c.90C>T synonymous_variant 0.17
fbiB 3642047 c.513G>C synonymous_variant 0.18
fbiB 3642299 p.Gln255His missense_variant 0.27
rpoA 3878492 p.Arg6Ser missense_variant 0.4
clpC1 4038890 p.Glu605Asp missense_variant 0.33
clpC1 4039994 p.Glu237Asp missense_variant 0.12
embC 4239879 p.Ala6Gly missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327065 p.Cys137Ser missense_variant 0.25
ethA 4327389 p.Thr29Pro missense_variant 0.6
ethA 4327400 p.Asp25Ala missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0