TB-Profiler result

Run: ERR2229605
Summary

Run ID: ERR2229605

Sample name:

Date: 31-03-2023 17:21:13

Number of reads: 1142611

Percentage reads mapped: 99.24

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 576108 p.Ala254Gly missense_variant 0.29
ccsA 620558 p.Gln223Arg missense_variant 0.11
rpoC 766956 p.Glu1196Ala missense_variant 0.22
rpoC 766970 p.Ala1201Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406780 c.561G>A 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
rrl 1474268 n.611C>T non_coding_transcript_exon_variant 0.15
rrl 1474808 n.1151G>A non_coding_transcript_exon_variant 0.14
tlyA 1917954 c.15C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 c.2868C>G synonymous_variant 0.16
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.51
Rv1979c 2222837 p.Ala110Thr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289517 c.-276C>G upstream_gene_variant 0.13
pncA 2289911 c.-670G>T upstream_gene_variant 0.14
kasA 2518317 p.Val68Asp missense_variant 0.14
kasA 2518864 c.750G>C synonymous_variant 0.16
ribD 2986971 p.Phe45Leu missense_variant 0.29
Rv2752c 3065437 p.Ala252Glu missense_variant 0.17
Rv2752c 3066279 c.-88A>C upstream_gene_variant 0.11
thyA 3074047 p.Ala142Glu missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.2
rpoA 3878657 c.-150C>T upstream_gene_variant 0.33
clpC1 4039161 p.His515Gly missense_variant 0.19
clpC1 4039169 p.Glu512Asp missense_variant 0.18
clpC1 4039324 p.Arg461Ser missense_variant 0.15
embC 4241492 p.Leu544Val missense_variant 1.0
embC 4241531 p.Ile557Leu missense_variant 0.12
embC 4241945 p.Arg695Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4249734 p.Pro1074His missense_variant 0.25
aftB 4268619 p.Val73Gly missense_variant 0.29
ubiA 4269232 p.Arg201His missense_variant 0.11
ethR 4327730 p.Phe61Ser missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0