TB-Profiler result

Run: ERR2228825
Summary

Run ID: ERR2228825

Sample name:

Date: 31-03-2023 16:22:15

Number of reads: 967398

Percentage reads mapped: 99.26

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 0.98
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 6435 p.Asn399Ser missense_variant 0.13
gyrA 7300 c.-2A>T upstream_gene_variant 0.31
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8762 c.1461G>T synonymous_variant 0.25
mshA 576440 p.Cys365Gly missense_variant 0.21
rpoB 759724 c.-83A>T upstream_gene_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304963 p.Trp678Ser missense_variant 0.15
embR 1416518 p.Leu277Arg missense_variant 0.32
embR 1417371 c.-24A>G upstream_gene_variant 0.14
atpE 1460898 c.-147T>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471910 n.65T>G non_coding_transcript_exon_variant 0.12
rrl 1473769 n.112T>C non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476161 n.2504A>T non_coding_transcript_exon_variant 0.3
rrl 1476162 n.2505A>T non_coding_transcript_exon_variant 0.22
rpsA 1834794 p.Tyr418Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918514 p.Val192Gly missense_variant 0.22
katG 2155722 c.390G>A synonymous_variant 0.17
PPE35 2168460 p.Asn718Ile missense_variant 0.38
PPE35 2168680 c.1932delT frameshift_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168738 c.1875T>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223141 c.24A>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518610 p.Thr166Pro missense_variant 0.33
ahpC 2726462 p.Glu90Asp missense_variant 0.25
pepQ 2859517 p.Gln301Arg missense_variant 0.12
Rv2752c 3064789 p.Leu468Ser missense_variant 0.11
Rv2752c 3065954 p.Thr80Pro missense_variant 0.18
thyX 3067839 p.Val36Ala missense_variant 0.12
thyA 3073804 p.Glu223Ala missense_variant 0.31
thyA 3074270 p.Asn68Asp missense_variant 0.33
thyA 3074281 p.Arg64Leu missense_variant 0.29
Rv3236c 3612506 p.His204Leu missense_variant 0.25
Rv3236c 3612939 p.Thr60Ser missense_variant 0.5
fbiB 3641953 p.Leu140Arg missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243944 p.Thr238Pro missense_variant 0.26
embB 4246736 p.Thr75Pro missense_variant 0.26
embB 4249653 p.His1047Pro missense_variant 0.2
embB 4249794 p.Ile1094Thr missense_variant 0.15
aftB 4267029 p.Asp603Val missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0