TB-Profiler result

Run: ERR2229322
Summary

Run ID: ERR2229322

Sample name:

Date: 31-03-2023 17:01:19

Number of reads: 964907

Percentage reads mapped: 98.82

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 7362 p.Glu21Gln missense_variant 1.0
gyrA 8750 c.1449C>A synonymous_variant 0.14
gyrA 8837 c.1536C>A synonymous_variant 0.12
gyrA 8846 c.1545C>T synonymous_variant 0.12
mshA 575411 p.Glu22Lys missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576262 c.915T>A synonymous_variant 0.17
ccsA 619823 c.-68C>A upstream_gene_variant 0.12
ccsA 620089 p.Gln67Glu missense_variant 0.33
ccsA 620772 p.Trp294Cys missense_variant 0.22
rpoB 761464 p.Val553Ala missense_variant 0.33
rpoB 762105 p.Ile767Phe missense_variant 0.15
rpoB 762624 p.Val940Ile missense_variant 0.13
rpoC 762974 c.-396G>A upstream_gene_variant 0.17
rpoC 763525 p.Phe52Leu missense_variant 0.33
rpoC 765733 c.2364G>T synonymous_variant 0.2
rpoC 765939 c.2573delA frameshift_variant 0.25
mmpL5 775586 c.2895A>G stop_lost&splice_region_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778884 p.Ala8Thr missense_variant 0.2
mmpR5 779028 p.Glu13Asp missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303164 c.234C>A synonymous_variant 0.12
fbiC 1303620 p.His230Gln missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416526 c.822C>G synonymous_variant 0.12
embR 1417539 c.-192G>C upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472298 n.453G>A non_coding_transcript_exon_variant 0.12
rrs 1472314 n.469A>T non_coding_transcript_exon_variant 0.12
rrs 1472421 n.576G>T non_coding_transcript_exon_variant 0.14
rrs 1472983 n.1138A>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
fabG1 1673977 p.Val180Leu missense_variant 0.2
inhA 1674731 p.Arg177His missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918598 p.Trp220* stop_gained 0.18
ndh 2101891 c.1152C>T synonymous_variant 0.13
ndh 2102624 p.Ser140Phe missense_variant 0.14
katG 2154767 p.Leu449Val missense_variant 0.12
katG 2154909 c.1203C>A synonymous_variant 0.29
katG 2155074 p.Ser346Arg missense_variant 0.12
katG 2155247 p.Glu289* stop_gained 0.15
katG 2156528 c.-417G>T upstream_gene_variant 0.13
PPE35 2167955 c.2658A>C synonymous_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2167997 c.2616G>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.71
PPE35 2170053 p.Thr187Ser missense_variant 0.75
Rv1979c 2222081 p.Ala362Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289157 p.Arg29Ser missense_variant 0.15
kasA 2518606 c.492G>C synonymous_variant 0.23
kasA 2518609 p.Met165Ile missense_variant 0.23
kasA 2518975 c.861C>A synonymous_variant 0.33
kasA 2519079 p.Glu322Ala missense_variant 0.25
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.2
kasA 2519153 p.Ile347Val missense_variant 0.2
folC 2746142 p.Pro486Leu missense_variant 0.14
folC 2747610 c.-12G>T upstream_gene_variant 0.2
folC 2747687 c.-89C>A upstream_gene_variant 0.25
pepQ 2859464 p.Gly319Ser missense_variant 0.14
ribD 2986777 c.-62C>G upstream_gene_variant 0.22
Rv2752c 3065792 p.Thr134Pro missense_variant 0.11
Rv2752c 3065825 p.Pro123Thr missense_variant 0.13
thyX 3067825 p.Arg41Trp missense_variant 0.22
thyA 3074097 c.375C>A synonymous_variant 0.12
ald 3086661 c.-159G>A upstream_gene_variant 0.13
ald 3087357 p.Gly180Ser missense_variant 0.17
fbiD 3339374 p.Glu86Ala missense_variant 0.18
fprA 3474573 c.567C>T synonymous_variant 0.17
Rv3236c 3612177 p.Arg314Trp missense_variant 0.25
fbiA 3640355 c.-188C>A upstream_gene_variant 0.17
fbiB 3640575 c.-960C>T upstream_gene_variant 0.15
fbiB 3641546 c.12C>T synonymous_variant 0.22
fbiB 3642198 p.Val222Met missense_variant 0.14
alr 3840466 p.Phe319Leu missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.17
rpoA 3877598 p.Leu304Met missense_variant 0.17
rpoA 3878366 p.Gly48* stop_gained 0.13
rpoA 3878609 c.-102T>A upstream_gene_variant 1.0
clpC1 4039161 p.His515Gly missense_variant 0.2
clpC1 4039169 p.Glu512Asp missense_variant 0.2
clpC1 4039265 p.Asp480Glu missense_variant 0.15
clpC1 4039575 p.Ala377Val missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.14
clpC1 4039682 c.1023C>T synonymous_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4039714 p.Tyr331His missense_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.22
clpC1 4040805 c.-101C>A upstream_gene_variant 0.12
embC 4240002 p.Thr47Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242936 p.Met1025Arg missense_variant 0.2
embA 4243835 c.603G>T synonymous_variant 0.29
embA 4244030 c.798C>T synonymous_variant 0.14
embA 4244540 c.1308G>T synonymous_variant 0.13
embA 4245097 p.Asn622Thr missense_variant 0.12
embA 4245471 p.Ala747Thr missense_variant 0.22
embA 4245690 p.Gly820Arg missense_variant 0.25
embB 4245884 c.-630C>T upstream_gene_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.9
embB 4246555 c.42G>C synonymous_variant 0.9
embB 4246556 p.Ala15Pro missense_variant 0.9
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.62
embB 4246618 c.105G>C synonymous_variant 0.11
embB 4248675 p.Ser721Tyr missense_variant 0.18
embB 4248958 p.Trp815Cys missense_variant 0.5
aftB 4268505 p.Arg111Gln missense_variant 0.15
ubiA 4269188 p.Thr216Ala missense_variant 0.18
ethA 4326322 c.1152T>C synonymous_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
ethA 4327187 p.Arg96Lys missense_variant 0.15
whiB6 4338406 p.Asp39Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407956 p.Arg83Trp missense_variant 0.29