TB-Profiler result

Run: ERR1950003
Summary

Run ID: ERR1950003

Sample name:

Date: 31-03-2023 15:37:04

Number of reads: 695086

Percentage reads mapped: 99.65

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 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 5161 c.-79C>G upstream_gene_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576499 c.1152G>A synonymous_variant 0.12
rpoB 762561 p.Arg919Trp missense_variant 0.33
rpoB 762628 p.Asp941Gly missense_variant 0.4
rpoC 764055 p.Leu229Pro missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777435 p.Ala349Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406355 p.Gln329Pro missense_variant 0.14
Rv1258c 1407238 p.Leu35Val missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471871 n.26C>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475844 n.2190_2193delAAGT non_coding_transcript_exon_variant 0.12
rrl 1475996 n.2339T>C non_coding_transcript_exon_variant 0.12
rrl 1476197 n.2540T>C non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918064 p.Pro42Gln missense_variant 0.14
katG 2155408 p.Pro235Leu missense_variant 0.12
katG 2155438 p.Met225Lys missense_variant 0.14
katG 2156393 c.-282G>A upstream_gene_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169449 p.Asn388Lys missense_variant 0.12
PPE35 2170029 p.Met195Arg missense_variant 0.25
Rv1979c 2222219 p.Asn316Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289032 c.210G>C synonymous_variant 0.12
eis 2714765 p.Leu190Met missense_variant 0.13
eis 2714858 p.Gly159Ser missense_variant 0.25
eis 2715050 p.Gly95Arg missense_variant 0.12
eis 2715153 c.180G>T synonymous_variant 0.11
ahpC 2726691 p.Ala167Ser missense_variant 0.14
folC 2747452 c.147G>A synonymous_variant 0.12
Rv2752c 3065452 p.Gln247Arg missense_variant 0.11
Rv3236c 3612636 p.Ala161Thr missense_variant 0.13
Rv3236c 3613144 c.-28G>C upstream_gene_variant 0.12
fbiB 3642460 p.Leu309Pro missense_variant 0.11
fbiB 3642570 p.Glu346* stop_gained 0.17
fbiB 3642650 c.1118dupT frameshift_variant 0.12
rpoA 3878310 c.198G>A synonymous_variant 0.12
clpC1 4040374 p.Gly111Cys missense_variant 0.14
panD 4043908 p.Pro125His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243065 p.Pro1068His missense_variant 0.12
embC 4243101 p.Val1080Glu missense_variant 0.11
embB 4246557 p.Ala15Glu missense_variant 0.22
embB 4247028 p.Leu172Gln missense_variant 0.2
embB 4247156 p.Thr215Pro missense_variant 0.18
embB 4247374 c.861C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407969 c.234A>G synonymous_variant 0.13
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0