TB-Profiler result

Run: ERR2229080
Summary

Run ID: ERR2229080

Sample name:

Date: 31-03-2023 16:36:48

Number of reads: 543643

Percentage reads mapped: 99.4

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
gyrA 7777 p.Arg159Pro missense_variant 0.22
gyrA 9384 p.Arg695Cys missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.3
ccsA 620755 p.Asp289Tyr missense_variant 0.25
rpoC 765473 p.Glu702Gln missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776003 c.2478C>T synonymous_variant 0.2
mmpL5 776008 p.His825Asp missense_variant 0.18
mmpL5 776009 c.2472A>G synonymous_variant 0.18
mmpS5 778832 p.Val25Ala missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801303 c.495G>A synonymous_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304491 c.1561_1562insGT frameshift_variant 0.2
Rv1258c 1407510 c.-170G>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472522 n.678delA non_coding_transcript_exon_variant 0.29
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.25
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
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 0.36
rpsA 1834225 c.684C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918662 c.723G>A synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.46
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2223285 c.-121T>A upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289000 p.Phe81Cys missense_variant 0.11
kasA 2518767 p.Thr218Asn missense_variant 0.18
eis 2714562 c.771T>C synonymous_variant 0.2
eis 2715040 p.Arg98His missense_variant 0.14
ribD 2987116 p.Tyr93Cys missense_variant 0.14
Rv2752c 3065491 p.Ile234Thr missense_variant 0.14
Rv2752c 3065665 p.Leu176* stop_gained 0.12
Rv2752c 3065976 p.Asp72Glu missense_variant 0.22
Rv3236c 3613217 c.-102delC upstream_gene_variant 0.12
fbiA 3640812 p.Gln90His missense_variant 0.29
fbiB 3641620 c.88_89delAG frameshift_variant 0.17
ddn 3986833 c.-11G>T upstream_gene_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.12
clpC1 4040455 p.Ala84Thr missense_variant 0.14
panD 4044375 c.-94T>A upstream_gene_variant 0.18
embC 4239716 c.-147G>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
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
aftB 4268465 c.372A>G synonymous_variant 0.22
aftB 4268500 p.Arg113Cys missense_variant 0.22
ethA 4326732 p.Ala248Pro missense_variant 0.2
ethA 4327154 p.Ala107Val missense_variant 0.18
ethA 4327920 c.-447A>T upstream_gene_variant 0.15
ethR 4327948 p.Val134Phe missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0