TB-Profiler result

Run: ERR2228897
Summary

Run ID: ERR2228897

Sample name:

Date: 31-03-2023 16:25:08

Number of reads: 386385

Percentage reads mapped: 98.44

Strain: lineage4

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
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 5055 c.-185A>T upstream_gene_variant 0.17
gyrB 7093 c.1856delA frameshift_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576114 p.Arg256Pro missense_variant 0.5
ccsA 620494 c.604C>A synonymous_variant 0.5
rpoB 761573 c.1769delT frameshift_variant 0.22
rpoB 762032 c.2226C>T synonymous_variant 0.18
rpoB 762550 p.Gly915Asp missense_variant 0.12
rpoB 763075 p.Thr1090Ile missense_variant 0.22
rpoC 764009 p.Arg214Ser missense_variant 0.22
rpoC 766481 c.3112C>A synonymous_variant 0.33
rpoC 766536 p.Glu1056Gly missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776146 p.Ala779Thr missense_variant 0.5
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpR5 778037 c.-953G>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305096 p.His722Gln missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471910 n.65T>C non_coding_transcript_exon_variant 0.17
rrs 1472852 n.1007G>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476062 n.2408dupA non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918662 c.723G>T synonymous_variant 0.25
ndh 2103178 c.-136G>C upstream_gene_variant 0.5
katG 2154372 p.Asp580Glu missense_variant 0.17
katG 2156131 c.-20C>A upstream_gene_variant 0.17
katG 2156558 c.-447G>A upstream_gene_variant 0.33
PPE35 2167760 c.2853G>A synonymous_variant 0.4
PPE35 2167763 p.Ile950Val missense_variant 0.4
PPE35 2168252 c.2361G>A synonymous_variant 0.67
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169308 c.1305C>T synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.27
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170284 p.Val110Ala missense_variant 0.14
Rv1979c 2221720 c.1445A>T stop_lost&splice_region_variant 0.12
Rv1979c 2223175 c.-11G>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518250 p.Leu46Ile missense_variant 0.25
kasA 2518552 c.441delC frameshift_variant 0.25
eis 2714179 p.Arg385Leu missense_variant 0.18
eis 2714560 p.Gly258Ala missense_variant 0.17
pepQ 2859581 p.Leu280Met missense_variant 0.25
Rv3236c 3612279 c.838C>T synonymous_variant 0.5
fbiA 3640640 p.Ala33Val missense_variant 0.29
fbiA 3640845 p.Trp101* stop_gained 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.24
rpoA 3877589 p.Ser307Thr missense_variant 0.25
ddn 3986982 p.Ala47Ser missense_variant 0.33
ddn 3987089 c.246G>C synonymous_variant 0.14
clpC1 4039077 p.Lys543Arg missense_variant 0.25
clpC1 4039468 p.Arg413Ser missense_variant 0.14
clpC1 4040010 p.Ala232Arg missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244505 p.Gly425Trp missense_variant 0.2
embA 4244761 p.Asn510Ile missense_variant 0.5
embA 4244942 p.Trp570Cys missense_variant 0.33
embB 4248401 p.Ala630Thr missense_variant 0.2
aftB 4267919 c.917_918insTA frameshift_variant 0.25
aftB 4268153 c.684G>T synonymous_variant 0.2
ubiA 4269110 c.723delC frameshift_variant 0.33
ubiA 4269116 p.Arg240Ser missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0