TB-Profiler result

Run: ERR2229027
Summary

Run ID: ERR2229027

Sample name:

Date: 31-03-2023 16:32:39

Number of reads: 1085644

Percentage reads mapped: 99.15

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 7165 c.-137C>A upstream_gene_variant 0.2
gyrB 7169 p.Ala644Ser missense_variant 0.18
gyrA 7323 p.Pro8Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491320 p.Ala180Ser missense_variant 0.22
ccsA 620482 p.Val198Leu missense_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 761868 p.Asp688Asn missense_variant 0.15
rpoC 764550 c.1184delG frameshift_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.12
mmpL5 776018 c.2463G>C synonymous_variant 0.15
mmpL5 776021 c.2460G>C synonymous_variant 0.15
mmpL5 776452 p.Gly677Ser missense_variant 0.18
mmpL5 777157 c.1324C>A synonymous_variant 0.14
mmpL5 777590 c.891G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781749 p.Thr64Ala missense_variant 0.12
fbiC 1302916 c.-15G>A upstream_gene_variant 0.13
fbiC 1303336 p.Ala136Pro missense_variant 0.25
fbiC 1303485 c.555C>T synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472241 n.396A>G non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.14
rrl 1476180 n.2523C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>T non_coding_transcript_exon_variant 0.12
rrl 1476376 n.2719G>A non_coding_transcript_exon_variant 0.15
rrl 1476390 n.2733G>T non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
fabG1 1673446 c.9delC frameshift_variant 0.12
fabG1 1673929 p.Ala164Ser missense_variant 0.14
fabG1 1673933 p.Arg165His missense_variant 0.15
inhA 1674375 c.174C>A synonymous_variant 0.25
rpsA 1833855 p.Lys105Ile missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918282 p.Tyr115His missense_variant 0.14
katG 2153935 p.Ala726Asp missense_variant 0.12
katG 2154825 c.1287G>T synonymous_variant 0.17
PPE35 2167689 p.Asn975Thr missense_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168043 p.Ala857Gly missense_variant 0.11
PPE35 2168047 p.Leu856Val missense_variant 0.22
PPE35 2168051 p.Val854Ile missense_variant 0.22
PPE35 2168059 p.Gln852Glu missense_variant 0.2
PPE35 2168068 p.Phe849Leu missense_variant 0.14
PPE35 2168070 p.Glu848Pro missense_variant 0.14
PPE35 2168140 p.Ala825Thr missense_variant 0.23
PPE35 2168143 p.Phe824Leu missense_variant 0.23
PPE35 2168150 c.2463T>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169209 c.1404C>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.24
PPE35 2169287 c.1326T>C synonymous_variant 0.26
PPE35 2169293 c.1320T>C synonymous_variant 0.17
PPE35 2169308 c.1305C>T synonymous_variant 0.25
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223198 c.-34G>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289861 c.-620A>G upstream_gene_variant 0.18
kasA 2518454 p.Thr114Ala missense_variant 0.14
kasA 2518606 c.492G>C synonymous_variant 0.14
kasA 2519252 p.Ile380Phe missense_variant 0.4
kasA 2519356 c.1242G>A synonymous_variant 0.29
kasA 2519359 c.1245T>G synonymous_variant 0.29
folC 2746453 c.1146G>A synonymous_variant 0.22
folC 2747444 p.Ala52Glu missense_variant 0.14
folC 2747552 c.46_47insAC frameshift_variant 0.17
thyA 3073769 c.703C>A synonymous_variant 0.21
fbiD 3339412 p.Ala99Ser missense_variant 0.14
Rv3083 3448315 c.-189C>A upstream_gene_variant 0.14
whiB7 3568795 c.-116A>T upstream_gene_variant 0.14
ddn 3986661 c.-183C>G upstream_gene_variant 0.12
clpC1 4039498 p.Ile403Val missense_variant 0.14
panD 4044332 c.-51C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244990 c.1758G>A synonymous_variant 0.12
embB 4245662 c.-852G>T upstream_gene_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.31
embB 4246747 p.Asp78Glu missense_variant 0.25
embB 4246858 c.345C>T synonymous_variant 0.5
embB 4249294 p.Lys927Asn missense_variant 0.17
ubiA 4269467 p.Asn123His missense_variant 0.14
aftB 4269471 c.-635C>G upstream_gene_variant 0.14
ubiA 4269818 p.Val6Leu missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethA 4327161 p.Ile105Phe missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407800 p.Val135Leu missense_variant 0.12
gid 4408216 c.-14C>T upstream_gene_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0