TB-Profiler result

Run: ERR2229507
Summary

Run ID: ERR2229507

Sample name:

Date: 31-03-2023 17:15:51

Number of reads: 739706

Percentage reads mapped: 99.36

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 6719 p.Asp494Asn missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575977 c.630G>A synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.67
rpoC 765844 c.2475C>A synonymous_variant 0.25
rpoC 765875 p.Val836Phe missense_variant 0.14
rpoC 767265 p.Ala1299Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777020 c.1461G>A synonymous_variant 0.17
mmpL5 777772 p.Val237Met missense_variant 0.12
mmpS5 778828 p.Gln26His missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303787 p.His286Arg missense_variant 0.14
atpE 1461002 c.-43G>T upstream_gene_variant 0.12
atpE 1461054 p.Thr4Ala missense_variant 0.15
atpE 1461086 c.42A>T synonymous_variant 0.13
atpE 1461146 c.102G>T synonymous_variant 0.11
atpE 1461173 c.129C>T synonymous_variant 0.12
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 0.2
fabG1 1673771 p.Ala111Asp missense_variant 0.12
rpsA 1834231 c.690T>G synonymous_variant 0.13
rpsA 1834393 p.Trp284Cys missense_variant 0.12
tlyA 1917840 c.-100C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101844 p.His400Leu missense_variant 0.12
ndh 2102644 c.399A>G synonymous_variant 0.29
katG 2154112 p.Thr667Asn missense_variant 0.13
katG 2154177 c.1935G>A synonymous_variant 0.13
katG 2154295 p.Ala606Asp missense_variant 0.15
katG 2155116 c.996C>T synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169557 c.1056C>T synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.23
PPE35 2170449 p.Gly55Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519041 c.927C>T synonymous_variant 0.2
kasA 2519223 p.Thr370Ile missense_variant 0.15
ahpC 2726177 c.-16G>T upstream_gene_variant 0.11
folC 2746220 p.Ala460Val missense_variant 0.14
folC 2746665 p.Phe312Leu missense_variant 0.33
folC 2746673 p.Val309Ala missense_variant 0.33
ribD 2986787 c.-52G>A upstream_gene_variant 0.14
Rv2752c 3065209 p.Leu328Ser missense_variant 0.17
thyX 3067193 c.753A>G stop_lost&splice_region_variant 0.11
Rv3236c 3612540 p.Leu193Ile missense_variant 0.25
Rv3236c 3612797 c.317_319delTGG disruptive_inframe_deletion 0.17
fbiA 3640874 p.Thr111Ile missense_variant 0.13
fbiB 3641377 c.-158C>A upstream_gene_variant 0.17
alr 3840852 p.Leu190Pro missense_variant 0.11
alr 3841085 p.Trp112Cys missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877541 p.Tyr323His missense_variant 0.1
clpC1 4038435 p.Ala757Glu missense_variant 0.15
clpC1 4038773 p.Asp644Glu missense_variant 0.14
clpC1 4038776 p.Glu643Asp missense_variant 0.14
clpC1 4039030 p.Lys559Glu missense_variant 0.15
clpC1 4039296 p.Ser470Leu missense_variant 0.11
clpC1 4039312 p.Glu465Gln missense_variant 0.12
clpC1 4040217 p.Gly163Val missense_variant 0.15
embC 4241577 p.Thr572Lys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245429 p.Cys733Arg missense_variant 0.11
embA 4245628 p.Pro799Leu missense_variant 0.2
embA 4245795 p.Ala855Ser missense_variant 0.11
embB 4245881 c.-633C>T upstream_gene_variant 0.13
embB 4245887 c.-627T>C upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.4
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4248319 c.1806A>T synonymous_variant 0.24
aftB 4267782 p.Val352Ala missense_variant 0.12
aftB 4268640 p.Leu66Pro missense_variant 0.25
aftB 4269051 c.-215C>A upstream_gene_variant 0.12
ethA 4326139 p.Glu445Asp missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0