TB-Profiler result

Run: ERR2229368
Summary

Run ID: ERR2229368

Sample name:

Date: 31-03-2023 17:06:53

Number of reads: 689560

Percentage reads mapped: 98.78

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 5710 c.471C>A synonymous_variant 0.14
gyrA 6739 c.-563C>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8808 p.Gly503* stop_gained 0.17
gyrA 9374 c.2073G>A synonymous_variant 0.18
fgd1 491290 p.Val170Leu missense_variant 0.22
ccsA 620112 p.Glu74Asp missense_variant 0.29
rpoC 765689 c.2320C>T synonymous_variant 0.22
rpoC 766211 p.Glu948* stop_gained 0.14
rpoC 766283 p.Thr972Ser missense_variant 0.4
rpoC 766447 c.3080delG frameshift_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775829 c.2652C>A synonymous_variant 0.29
mmpL5 775883 c.2598C>T synonymous_variant 0.22
mmpL5 775955 p.Ile842Val missense_variant 0.2
mmpL5 776009 c.2472A>G synonymous_variant 0.22
mmpL5 776018 c.2463G>C synonymous_variant 0.18
mmpL5 776021 c.2460G>C synonymous_variant 0.18
mmpL5 776080 p.Ala801Ser missense_variant 0.22
mmpL5 776081 c.2400G>A synonymous_variant 0.22
mmpR5 779008 p.Val7Ile missense_variant 0.15
mmpR5 779046 p.Phe19Leu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781481 c.-79C>A upstream_gene_variant 0.29
fbiC 1303302 c.372A>G synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304844 c.1914C>T synonymous_variant 0.29
Rv1258c 1407056 c.285G>A synonymous_variant 0.2
embR 1417373 c.-26G>A upstream_gene_variant 0.29
atpE 1461280 p.Pro79Leu missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472178 n.333C>A non_coding_transcript_exon_variant 0.18
rrs 1473156 n.1311A>G non_coding_transcript_exon_variant 0.14
rrl 1473477 n.-181T>C upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474544 n.887G>T non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.25
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
rpsA 1833733 c.192C>A synonymous_variant 0.25
rpsA 1833909 p.Asp123Val missense_variant 0.17
tlyA 1917874 c.-66G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101974 p.Ala357Ser missense_variant 0.22
ndh 2102371 p.Met224Ile missense_variant 0.33
ndh 2102890 p.Phe51Leu missense_variant 0.25
ndh 2103165 c.-123G>A upstream_gene_variant 0.2
katG 2155191 c.921A>C synonymous_variant 0.15
PPE35 2167833 p.Leu927Arg missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.27
PPE35 2169281 c.1332T>G synonymous_variant 0.31
PPE35 2169287 c.1326T>C synonymous_variant 0.35
PPE35 2169293 c.1320T>C synonymous_variant 0.2
PPE35 2169302 p.Met437Ile missense_variant 0.12
PPE35 2169308 c.1305C>T synonymous_variant 0.12
PPE35 2169457 p.His386Asp missense_variant 0.15
PPE35 2169488 c.1125G>C synonymous_variant 0.16
PPE35 2169902 c.711G>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.78
PPE35 2170053 p.Thr187Ser missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289521 c.-280G>T upstream_gene_variant 0.2
pncA 2290069 c.-828C>T upstream_gene_variant 0.17
kasA 2518204 c.90G>A synonymous_variant 0.25
kasA 2518481 p.Val123Ile missense_variant 0.29
kasA 2518809 p.Lys232Arg missense_variant 0.18
eis 2714673 c.660C>A synonymous_variant 0.33
eis 2714837 p.Val166Phe missense_variant 0.2
ahpC 2726009 c.-184T>A upstream_gene_variant 0.2
ahpC 2726515 p.Phe108Ser missense_variant 0.18
folC 2747384 p.Thr72Ile missense_variant 0.25
folC 2747797 c.-199T>A upstream_gene_variant 0.3
pepQ 2860303 p.Ser39Tyr missense_variant 0.29
Rv2752c 3065198 p.Asp332Tyr missense_variant 0.17
thyX 3067306 p.Glu214Lys missense_variant 0.15
thyA 3074375 p.Gln33Lys missense_variant 0.29
fprA 3474663 p.Asp219Glu missense_variant 0.25
Rv3236c 3612086 p.Ala344Gly missense_variant 0.18
Rv3236c 3612958 c.159C>A synonymous_variant 0.25
Rv3236c 3613264 c.-148G>A upstream_gene_variant 0.33
Rv3236c 3613266 c.-150G>T upstream_gene_variant 0.33
alr 3840422 c.999A>G synonymous_variant 0.33
alr 3841546 c.-126C>A upstream_gene_variant 0.37
rpoA 3877549 p.Val320Ala missense_variant 0.13
rpoA 3878486 p.Thr8Pro missense_variant 0.29
clpC1 4038313 p.Gln798Glu missense_variant 0.33
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245469 p.Asn746Ser missense_variant 0.5
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.64
embB 4246556 p.Ala15Pro missense_variant 0.64
embB 4246563 p.Leu17Trp missense_variant 0.38
embB 4248215 p.Arg568Ser missense_variant 0.14
embB 4249045 p.Leu844Phe missense_variant 0.5
aftB 4267087 p.Leu584Met missense_variant 0.2
aftB 4268493 c.343delG frameshift_variant 0.13
aftB 4268937 c.-101T>A upstream_gene_variant 0.33
aftB 4269516 c.-680G>C upstream_gene_variant 0.25
ethA 4326386 p.Ile363Thr missense_variant 0.12
ethA 4328379 c.-906C>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0