TB-Profiler result

Run: ERR1949965

Summary

Run ID: ERR1949965

Sample name:

Date: 31-03-2023 15:35:51

Number of reads: 1154099

Percentage reads mapped: 99.34

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 0.99
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 6165 p.Asn309Thr missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8774 c.1473C>T synonymous_variant 0.15
fgd1 491173 p.Arg131Gly missense_variant 0.14
fgd1 491315 p.Gly178Ala missense_variant 0.33
fgd1 491414 p.Val211Glu missense_variant 0.29
ccsA 619738 c.-153T>G upstream_gene_variant 0.19
ccsA 619821 c.-70T>C upstream_gene_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776359 p.Phe708Ile missense_variant 0.25
mmpS5 778577 p.Thr110Ser missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304033 p.Glu368Gly missense_variant 0.12
Rv1258c 1407066 p.Val92Gly missense_variant 0.2
Rv1258c 1407472 c.-132T>G upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472898 n.1053T>A non_coding_transcript_exon_variant 0.17
rrl 1473888 n.231T>C non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474017 n.360A>T non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169685 p.Gly310Arg missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2222923 p.Tyr81Cys missense_variant 0.11
Rv1979c 2223075 c.90C>T synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518695 p.Val194Gly missense_variant 0.2
ahpC 2726428 p.Asp79Ala missense_variant 0.17
pepQ 2859904 p.Val172Gly missense_variant 0.13
Rv2752c 3065752 p.Asn147Ser missense_variant 0.22
Rv2752c 3067069 c.-878T>A upstream_gene_variant 0.18
thyX 3068151 c.-206T>G upstream_gene_variant 0.17
fprA 3475134 c.1128A>G synonymous_variant 0.12
Rv3236c 3612568 c.549G>A synonymous_variant 0.33
fbiA 3641444 p.Val301Gly missense_variant 0.19
fbiB 3642505 p.Asp324Ala missense_variant 0.29
rpoA 3878496 c.12A>C synonymous_variant 0.13
clpC1 4039567 p.Val380Leu missense_variant 0.47
embC 4240581 p.Leu240Arg missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4249677 p.Arg1055Leu missense_variant 0.17
ethR 4328104 p.Ser186Ala missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0