TB-Profiler result

Run: ERR2229476
Summary

Run ID: ERR2229476

Sample name:

Date: 31-03-2023 17:14:26

Number of reads: 552087

Percentage reads mapped: 99.41

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
gyrA 6400 c.-902C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7445 c.144C>T synonymous_variant 0.25
gyrA 7446 p.Lys49Glu missense_variant 0.25
gyrA 9611 c.2310C>T synonymous_variant 0.15
fgd1 491220 c.438C>T synonymous_variant 0.33
rpoB 761909 c.2103T>C synonymous_variant 0.18
rpoC 762758 c.-612G>A upstream_gene_variant 0.13
rpoC 765142 p.Glu591Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775955 p.Ile842Val missense_variant 0.15
mmpL5 776616 p.Pro622Leu missense_variant 0.15
mmpL5 776660 c.1820delT frameshift_variant 0.12
mmpL5 776760 p.Phe574Tyr missense_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801372 p.Glu188Asp missense_variant 0.12
fbiC 1303295 p.Tyr122Ser missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417431 c.-84C>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472454 n.609C>A non_coding_transcript_exon_variant 0.12
rrs 1473236 n.1393dupC non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
inhA 1673697 c.-505G>T upstream_gene_variant 0.15
rpsA 1833585 p.Asp15Gly missense_variant 0.12
rpsA 1834778 p.Glu413Lys missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154370 p.Val581Ala missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169373 p.Thr414Ala missense_variant 0.12
PPE35 2169890 c.723C>T synonymous_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170147 p.Ser156Ala missense_variant 0.23
PPE35 2170159 p.Ala152Ser missense_variant 0.14
PPE35 2170164 p.Ala150Val missense_variant 0.14
PPE35 2170235 c.378T>C synonymous_variant 0.13
PPE35 2170238 c.375T>G synonymous_variant 0.13
PPE35 2170244 c.369G>A synonymous_variant 0.13
PPE35 2170249 p.Ile122Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288849 c.390_392delGGT disruptive_inframe_deletion 0.14
pncA 2289539 c.-298C>T upstream_gene_variant 0.25
pncA 2289893 c.-652C>T upstream_gene_variant 0.15
kasA 2518026 c.-89G>T upstream_gene_variant 0.13
ribD 2987153 p.His105Gln missense_variant 0.17
thyX 3067426 p.Val174Met missense_variant 0.17
thyA 3074508 c.-37C>T upstream_gene_variant 0.22
fprA 3474151 p.Val49Met missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.19
embC 4240135 c.273C>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243770 p.Gly180Arg missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.43
aftB 4268687 c.150C>T synonymous_variant 0.18
aftB 4268733 p.Leu35Pro missense_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326964 c.-585G>A upstream_gene_variant 0.12
ethR 4326970 c.-579G>T upstream_gene_variant 0.13
ethR 4327601 p.Ala18Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0