TB-Profiler result

Run: ERR2229055
Summary

Run ID: ERR2229055

Sample name:

Date: 31-03-2023 16:34:03

Number of reads: 958359

Percentage reads mapped: 99.33

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9235 p.Ser645Leu missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.43
rpoB 761702 c.1896C>A synonymous_variant 0.13
rpoC 766676 p.Asp1103Asn missense_variant 0.14
rpoC 766901 p.Gly1178Arg missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473644 n.-14G>T upstream_gene_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475623 n.1966C>G non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102759 p.Ala95Asp missense_variant 0.17
katG 2153985 p.Glu709Asp missense_variant 0.12
katG 2155423 p.Val230Glu missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.4
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170574 c.39C>G synonymous_variant 0.12
PPE35 2170580 c.33C>T synonymous_variant 0.12
PPE35 2170589 c.24G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518592 p.Ala160Thr missense_variant 0.18
kasA 2519339 p.Val409Leu missense_variant 0.14
Rv2752c 3064953 c.1239C>A synonymous_variant 0.12
Rv2752c 3065277 c.915C>A synonymous_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.31
ald 3087442 p.Asp208Val missense_variant 0.25
ald 3087811 p.Ala331Glu missense_variant 0.18
fprA 3474036 c.30C>A synonymous_variant 0.17
fprA 3474366 c.360G>C synonymous_variant 0.14
fprA 3474907 c.901C>A synonymous_variant 0.4
Rv3236c 3613050 p.Ala23Ser missense_variant 0.14
fbiA 3640685 p.Gly48Ala missense_variant 0.11
fbiB 3641536 c.2T>C start_lost 0.12
fbiB 3641689 p.Val52Glu missense_variant 0.15
fbiB 3642223 p.Arg230Gln missense_variant 0.12
alr 3840271 p.Gly384Ser missense_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3877733 c.775C>A synonymous_variant 0.14
clpC1 4038211 c.2494C>T synonymous_variant 0.14
clpC1 4040018 c.687G>A synonymous_variant 0.14
embC 4239664 c.-199C>A upstream_gene_variant 0.15
embC 4240211 p.Val117Phe missense_variant 0.12
embC 4241369 p.Lys503Gln missense_variant 0.13
embC 4241416 c.1554C>A synonymous_variant 0.12
embC 4241455 c.1593C>T synonymous_variant 0.15
embC 4242345 p.Ala828Asp missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242919 c.-314A>G upstream_gene_variant 0.11
embA 4244935 p.Thr568Asn missense_variant 0.22
embB 4246567 c.54_55insT frameshift_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.15
embB 4249104 c.2593delC frameshift_variant 0.14
ubiA 4269864 c.-32delG upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0