TB-Profiler result

Run: ERR2229320
Summary

Run ID: ERR2229320

Sample name:

Date: 31-03-2023 17:00:30

Number of reads: 952932

Percentage reads mapped: 98.84

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 6199 p.Phe320Leu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.44
mshA 576469 c.1122G>T synonymous_variant 0.15
mshA 576497 p.Gly384Trp missense_variant 0.25
ccsA 620484 c.594G>A synonymous_variant 0.13
rpoB 759749 c.-57delG upstream_gene_variant 0.18
rpoC 764359 c.990C>G synonymous_variant 0.15
rpoC 765637 c.2268C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776008 p.His825Asp missense_variant 0.17
mmpL5 776730 p.Tyr584Ser missense_variant 0.18
mmpL5 776739 p.Ile581Asn missense_variant 0.15
mmpL5 777032 c.1449C>G synonymous_variant 0.13
mmpL5 777035 c.1446G>A synonymous_variant 0.13
mmpL5 777042 p.Arg480Gln missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801303 c.495G>A synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304484 c.1554C>T synonymous_variant 0.12
fbiC 1304745 c.1815C>T synonymous_variant 0.12
fbiC 1304935 p.Ala669Thr missense_variant 0.12
Rv1258c 1406599 p.Pro248Ser missense_variant 0.15
atpE 1460851 c.-194T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
tlyA 1917785 c.-155C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155419 p.Asn231Lys missense_variant 0.13
katG 2155756 p.Arg119His missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.25
PPE35 2167967 c.2646A>C synonymous_variant 0.25
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169025 p.Pro530Ser missense_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2169596 c.1017T>C synonymous_variant 0.14
PPE35 2169602 c.1011C>A synonymous_variant 0.19
PPE35 2169732 p.Asn294Ser missense_variant 0.21
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.66
PPE35 2170053 p.Thr187Ser missense_variant 0.66
PPE35 2170392 p.Gly74Ala missense_variant 0.17
PPE35 2170400 c.213G>C synonymous_variant 0.16
Rv1979c 2222683 p.Trp161Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289813 c.-573_-572insT upstream_gene_variant 0.15
pncA 2289817 c.-577_-576delTTinsGC upstream_gene_variant 0.15
pncA 2290158 c.-917C>T upstream_gene_variant 0.2
kasA 2519128 c.1014G>C synonymous_variant 0.13
kasA 2519131 c.1017G>C synonymous_variant 0.14
eis 2714853 c.480C>T synonymous_variant 0.18
folC 2746399 c.1200C>T synonymous_variant 0.15
folC 2746621 c.978C>G synonymous_variant 0.18
folC 2747676 c.-78C>A upstream_gene_variant 0.15
ribD 2986778 c.-61G>T upstream_gene_variant 0.14
Rv2752c 3065598 c.594G>T synonymous_variant 0.17
thyA 3074200 p.Gly91Val missense_variant 0.14
fbiB 3641421 c.-114C>A upstream_gene_variant 0.25
fbiB 3642587 p.Met351Ile missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.16
panD 4043982 c.300A>G synonymous_variant 0.11
embC 4241152 c.1290C>A synonymous_variant 0.13
embC 4242128 p.Leu756Met missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4249381 c.2868A>C synonymous_variant 0.12
aftB 4268820 p.Leu6Ser missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0