TB-Profiler result

Run: ERR2229641

Summary

Run ID: ERR2229641

Sample name:

Date: 31-03-2023 17:23:10

Number of reads: 787458

Percentage reads mapped: 99.27

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
mshA 575261 c.-87T>C upstream_gene_variant 0.13
mshA 576586 c.1239G>T synonymous_variant 0.15
rpoB 759853 p.Ser16Ile missense_variant 0.11
rpoB 760734 p.Val310Phe missense_variant 0.29
rpoB 760770 p.Ile322Val missense_variant 0.18
rpoB 760908 p.Gly368Ser missense_variant 0.29
rpoB 760935 p.Glu377Lys missense_variant 0.22
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoB 761463 p.Val553Met missense_variant 0.12
rpoB 762218 c.2412T>C synonymous_variant 0.11
rpoB 763014 p.Met1070Leu missense_variant 0.12
rpoC 763548 p.Cys60Tyr missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776238 p.Gly748Asp missense_variant 0.18
mmpL5 776404 p.Pro693Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781641 p.Pro28Ser missense_variant 0.12
rplC 801118 p.Glu104Arg missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406751 p.Gly197Asp missense_variant 0.17
Rv1258c 1406861 c.480C>A synonymous_variant 0.12
atpE 1460852 c.-193C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1834319 p.Val260Ile missense_variant 0.2
rpsA 1834560 p.Val340Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102185 c.858C>T synonymous_variant 0.13
katG 2155412 p.Gly234Trp missense_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.12
PPE35 2168114 c.2499T>C synonymous_variant 0.18
PPE35 2168373 p.Pro747Gln missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519045 p.His311Asn missense_variant 0.14
eis 2714326 p.Gly336Ala missense_variant 0.11
eis 2714542 p.Arg264Leu missense_variant 0.12
pepQ 2860265 p.Ala52Ser missense_variant 0.17
ribD 2987440 p.Thr201Lys missense_variant 0.12
whiB7 3568528 p.Gln51Arg missense_variant 0.18
fbiB 3640863 c.-672C>T upstream_gene_variant 0.12
fbiB 3642318 p.Ser262Pro missense_variant 0.12
alr 3840547 p.Gly292Ser missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.26
clpC1 4038683 c.2022T>C synonymous_variant 0.11
clpC1 4039366 p.Ala447Ser missense_variant 0.15
embC 4240868 p.His336Tyr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4247291 p.Ser260Thr missense_variant 0.15
embB 4248477 p.Pro655Arg missense_variant 0.11
embB 4249398 p.Ala962Val missense_variant 0.12
aftB 4267217 c.1620C>T synonymous_variant 0.12
ubiA 4269162 p.Leu224Phe missense_variant 0.17
ethA 4327427 p.Gly16Ala missense_variant 0.11
ethA 4327647 c.-174G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0