TB-Profiler result

Run: ERR2229134
Summary

Run ID: ERR2229134

Sample name:

Date: 31-03-2023 16:43:02

Number of reads: 578001

Percentage reads mapped: 99.52

Strain: lineage4.8

Drug-resistance: HR-TB

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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
katG 2155289 p.Thr275Ser missense_variant 0.29 isoniazid
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 5622 p.Val128Asp missense_variant 0.12
gyrB 5625 p.Asn129Ser missense_variant 0.12
gyrB 5630 c.391C>T synonymous_variant 0.12
gyrB 5633 p.Ser132Thr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8156 c.855T>C synonymous_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576420 p.Val358Asp missense_variant 0.11
rpoB 760425 p.Glu207Lys missense_variant 0.18
rpoB 760495 p.Val230Ala missense_variant 0.14
rpoB 761129 c.1323G>C synonymous_variant 0.13
rpoC 764084 p.Asn239Asp missense_variant 0.18
rpoC 766145 p.Gly926Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775864 p.Ala873Thr missense_variant 0.2
mmpL5 776059 p.Val808Met missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1417468 c.-121G>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472597 n.752G>T non_coding_transcript_exon_variant 0.4
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475907 n.2250G>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
inhA 1674534 c.333G>T synonymous_variant 0.25
inhA 1674685 p.Thr162Ala missense_variant 0.1
rpsA 1833569 p.Gln10Lys missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102003 p.Ile347Asn missense_variant 0.33
katG 2154711 c.1401G>A synonymous_variant 0.13
PPE35 2167847 c.2766A>C synonymous_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167878 p.Ser912Asn missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168870 c.1743G>T synonymous_variant 0.17
PPE35 2169056 c.1557A>T synonymous_variant 0.33
PPE35 2170035 p.Val193Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170392 p.Gly74Ala missense_variant 0.11
PPE35 2170400 c.213G>C synonymous_variant 0.11
Rv1979c 2221925 p.Asp414Asn missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289005 c.237G>A synonymous_variant 0.13
ribD 2986650 c.-189G>C upstream_gene_variant 0.11
ald 3086902 p.Arg28Pro missense_variant 0.14
whiB7 3568458 c.222C>T synonymous_variant 0.18
whiB7 3568678 p.Val1Ala missense_variant 0.2
Rv3236c 3613159 c.-43G>A upstream_gene_variant 0.22
fbiA 3640681 p.Val47Ile missense_variant 0.11
alr 3840645 p.Gly259Glu missense_variant 0.14
rpoA 3877655 p.Asp285His missense_variant 0.14
ddn 3986761 c.-83T>A upstream_gene_variant 0.11
ddn 3986849 c.9delA frameshift_variant 0.13
clpC1 4038581 c.2124G>A synonymous_variant 0.11
clpC1 4039674 p.Pro344Gln missense_variant 0.12
clpC1 4039676 c.1029G>A synonymous_variant 0.12
clpC1 4039682 c.1023C>T synonymous_variant 0.12
clpC1 4039774 p.Lys311* stop_gained 0.22
embC 4241035 c.1173G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4248298 p.His595Gln missense_variant 0.17
embB 4249736 p.Pro1075Ala missense_variant 0.4
ethA 4327262 p.Gly71Val missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0