TB-Profiler result

Run: ERR2229545
Summary

Run ID: ERR2229545

Sample name:

Date: 31-03-2023 17:18:16

Number of reads: 1125143

Percentage reads mapped: 99.07

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 0.21
rpoC 764186 p.Glu273* stop_gained 0.12
rpoC 765427 p.Lys686Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777062 c.1419C>T synonymous_variant 0.17
mmpL5 777157 c.1324C>A synonymous_variant 0.2
mmpL5 777164 c.1317C>T synonymous_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406283 p.Thr353Met missense_variant 0.13
embR 1416894 p.Asp152Tyr missense_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 1475324 n.1668delC non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102175 p.Ala290Ser missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170392 p.Gly74Ala missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289953 c.-712C>T upstream_gene_variant 0.12
kasA 2518268 p.Thr52Ala missense_variant 0.18
kasA 2518393 p.Gln93His missense_variant 0.1
kasA 2518395 p.Leu94Pro missense_variant 0.1
kasA 2519078 p.Glu322Leu missense_variant 0.12
kasA 2519083 c.970_976delAACGCCA frameshift_variant 0.17
kasA 2519097 p.Val328Gly missense_variant 0.15
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.14
eis 2714783 p.Gln184* stop_gained 0.18
ribD 2987528 c.690A>G synonymous_variant 0.2
Rv2752c 3064585 p.Thr536Met missense_variant 0.11
Rv2752c 3064721 p.His491Tyr missense_variant 0.13
fbiB 3641716 p.Val61Ala missense_variant 0.11
fbiB 3642766 p.Glu411Val missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.16
embC 4240651 c.789G>C synonymous_variant 0.12
embC 4242143 p.Pro761Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243410 p.Ala60Ser missense_variant 0.13
embB 4246094 c.-420C>T upstream_gene_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.8
embB 4246556 p.Ala15Pro missense_variant 0.8
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.6
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4248739 c.2226G>T synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0