TB-Profiler result

Run: ERR2228977
Summary

Run ID: ERR2228977

Sample name:

Date: 31-03-2023 16:29:02

Number of reads: 840531

Percentage reads mapped: 99.27

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 2155327 c.784delA frameshift_variant 0.22 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 7178 c.-124T>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7928 c.627C>T synonymous_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.28
ccsA 619697 c.-194A>G upstream_gene_variant 0.14
ccsA 620169 c.279G>T synonymous_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406944 p.Ala133Ser missense_variant 0.11
embR 1416751 p.Phe199Leu missense_variant 0.13
atpE 1461069 c.28delC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.28
fabG1 1673349 c.-91G>C upstream_gene_variant 0.26
fabG1 1673357 c.-83G>A upstream_gene_variant 0.19
fabG1 1673359 c.-81T>C upstream_gene_variant 0.21
fabG1 1673361 c.-79C>G upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
inhA 1673622 c.-580C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918680 c.741C>A synonymous_variant 0.12
ndh 2102910 p.Arg45Ser missense_variant 0.13
katG 2153910 c.2202C>T synonymous_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169322 c.1291T>C synonymous_variant 0.11
PPE35 2169323 c.1290C>G synonymous_variant 0.11
PPE35 2169337 p.Asp426His missense_variant 0.13
PPE35 2169671 c.942C>G synonymous_variant 0.14
PPE35 2169695 c.918A>G synonymous_variant 0.1
PPE35 2169704 c.909A>C synonymous_variant 0.16
PPE35 2169707 c.906T>C synonymous_variant 0.11
PPE35 2169710 c.903G>T synonymous_variant 0.11
PPE35 2169717 p.Asn299Ile missense_variant 0.17
PPE35 2169725 c.888T>C synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170528 p.Ser29Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518677 c.569_574delCCGACG disruptive_inframe_deletion 0.12
kasA 2518692 p.Ala193Gly missense_variant 0.12
kasA 2518705 c.591T>A synonymous_variant 0.13
kasA 2518879 c.765A>G synonymous_variant 0.13
kasA 2518882 c.768C>A synonymous_variant 0.13
eis 2714990 p.Val115Phe missense_variant 0.15
thyX 3067655 c.291G>A synonymous_variant 0.25
ald 3087879 c.1060C>A synonymous_variant 0.2
fprA 3473864 c.-143G>T upstream_gene_variant 0.12
fbiA 3640880 p.Leu113Arg missense_variant 0.13
fbiA 3640888 c.349delC frameshift_variant 0.13
rpoA 3878439 c.69C>T synonymous_variant 0.15
rpoA 3878492 p.Arg6Cys missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.11
clpC1 4039654 p.Thr351Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242694 c.-539G>A upstream_gene_variant 0.18
embA 4244319 p.Thr363Ser missense_variant 0.12
embA 4244418 p.Val396Leu missense_variant 0.15
embA 4245522 p.Leu764Met missense_variant 0.13
embA 4245745 c.2515delG frameshift_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.56
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.44
ethA 4327248 p.Ala76Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0