TB-Profiler result

Run: ERR2229248
Summary

Run ID: ERR2229248

Sample name:

Date: 31-03-2023 16:53:01

Number of reads: 962048

Percentage reads mapped: 99.25

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 0.6
ccsA 620098 c.208C>A synonymous_variant 0.17
ccsA 620314 p.Leu142Met missense_variant 0.14
rpoB 759816 c.13dupC frameshift_variant 0.14
rpoC 764664 p.Val432Gly missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775800 p.Ser894Leu missense_variant 0.14
mmpL5 776087 c.2394C>G synonymous_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 0.17
mmpL5 778907 c.-427C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303684 p.Ser252Thr missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472870 n.1027dupG non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474922 n.1265G>T non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
rpsA 1833956 p.Ile139Phe missense_variant 0.12
rpsA 1834138 c.597C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154673 p.Ala480Gly missense_variant 0.12
katG 2154827 p.Pro429Thr missense_variant 0.15
PPE35 2167745 p.Thr956Arg missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289345 c.-104G>A upstream_gene_variant 0.12
kasA 2518841 p.Gly243Cys missense_variant 0.13
folC 2746787 p.Ala271Val missense_variant 0.2
pepQ 2859424 p.Gly332Ala missense_variant 0.13
pepQ 2860114 p.Val102Gly missense_variant 0.25
thyA 3074343 c.129G>T synonymous_variant 0.17
ald 3087582 p.Val255Phe missense_variant 0.25
ald 3087818 c.999C>T synonymous_variant 0.15
whiB7 3568748 c.-69C>A upstream_gene_variant 0.12
Rv3236c 3613279 c.-163C>T upstream_gene_variant 0.17
fbiB 3642670 p.Ala379Val missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4038595 p.His704Asn missense_variant 0.12
clpC1 4039829 p.Leu292Phe missense_variant 0.17
panD 4044469 c.-188G>A upstream_gene_variant 0.14
embC 4242491 c.2632_2638delGACAGGG frameshift_variant 0.25
embC 4242502 c.2642_2643insCTGTCCC frameshift_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244454 p.Ala408Thr missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.39
embB 4246556 p.Ala15Pro missense_variant 0.39
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4247215 c.702C>T synonymous_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.13
ethR 4328041 p.Thr165Pro missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407804 c.399T>C synonymous_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0