TB-Profiler result

Run: ERR2229555
Summary

Run ID: ERR2229555

Sample name:

Date: 31-03-2023 17:18:53

Number of reads: 817874

Percentage reads mapped: 99.42

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 0.99
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 2154550 c.1561delC frameshift_variant 0.12 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7855 p.Met185Lys missense_variant 0.22
mshA 575176 c.-172T>A upstream_gene_variant 0.22
ccsA 619861 c.-30A>T upstream_gene_variant 0.29
ccsA 620582 p.Arg231Gln missense_variant 0.12
ccsA 620732 p.Ala281Glu missense_variant 0.13
rpoC 766137 p.Arg923Gln missense_variant 0.14
rpoC 766642 c.3273C>T synonymous_variant 0.2
rpoC 766859 p.Arg1164Trp missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775826 c.2655G>C synonymous_variant 0.12
mmpL5 777746 c.735G>T synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781410 c.-150G>A upstream_gene_variant 0.12
rplC 801248 p.Arg147His missense_variant 0.15
fbiC 1303676 p.Gly249Asp missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1460860 c.-185C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474772 n.1115C>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.21
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
rpsA 1834345 p.Asp268Glu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918258 p.His107Tyr missense_variant 0.17
ndh 2102357 p.Gly229Asp missense_variant 0.25
ndh 2102389 c.654G>C synonymous_variant 0.25
ndh 2102392 c.651C>A synonymous_variant 0.25
katG 2155920 c.192T>C synonymous_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.16
PPE35 2167833 p.Leu927Arg missense_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170159 p.Ala152Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288978 c.264G>A synonymous_variant 0.13
kasA 2518597 c.483C>T synonymous_variant 0.29
ribD 2987064 p.Glu76* stop_gained 0.15
Rv2752c 3066076 p.Arg39Leu missense_variant 0.15
Rv2752c 3066134 p.Ala20Ser missense_variant 0.14
thyX 3067366 p.His194Asp missense_variant 0.14
thyX 3067870 p.Thr26Ser missense_variant 0.29
thyX 3067924 p.Arg8Cys missense_variant 0.18
ald 3087332 c.513C>T synonymous_variant 0.25
fprA 3473968 c.-39C>A upstream_gene_variant 0.18
fprA 3474134 p.Pro43Leu missense_variant 0.15
Rv3236c 3612308 p.Phe270Ser missense_variant 0.17
fbiA 3641515 p.Asp325Tyr missense_variant 0.15
fbiB 3641811 p.Leu93Val missense_variant 0.18
fbiB 3642349 p.Pro272Leu missense_variant 0.15
fbiB 3642385 p.Leu284His missense_variant 0.18
alr 3840812 c.609T>C synonymous_variant 0.11
alr 3841119 p.Arg101Leu missense_variant 0.13
ddn 3986771 c.-73A>T upstream_gene_variant 0.25
clpC1 4038562 p.Asp715Tyr missense_variant 0.18
clpC1 4039042 p.Ser555Thr missense_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243375 p.Gly48Asp missense_variant 0.14
embA 4244295 p.Ala355Ser missense_variant 0.29
embA 4244957 c.1725C>T synonymous_variant 0.18
embA 4245166 p.Pro645Gln missense_variant 0.12
embA 4245667 p.Thr812Asn missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.56
embB 4246563 p.Leu17Trp missense_variant 0.27
embB 4249764 p.Thr1084Asn missense_variant 0.29
aftB 4268267 c.570G>T synonymous_variant 0.12
aftB 4268609 c.228G>A synonymous_variant 0.14
aftB 4268806 p.Thr11Ala missense_variant 0.2
aftB 4268879 c.-43G>T upstream_gene_variant 0.12
ubiA 4269469 p.Pro122Leu missense_variant 0.17
aftB 4269630 c.-794G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0