TB-Profiler result

Run: ERR2229340
Summary

Run ID: ERR2229340

Sample name:

Date: 31-03-2023 17:02:30

Number of reads: 1176906

Percentage reads mapped: 98.85

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
rpoB 760769 c.963C>A synonymous_variant 0.18
rpoB 760790 c.984C>A synonymous_variant 0.13
rpoB 760954 p.Ile383Thr missense_variant 0.11
rpoB 761465 c.1659G>A synonymous_variant 0.12
rpoC 764148 p.Ser260* stop_gained 0.12
rpoC 764176 p.Asp269Glu missense_variant 0.14
rpoC 764630 p.Arg421Ser missense_variant 0.17
rpoC 765416 p.Phe683Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777000 p.His494Leu missense_variant 0.2
mmpL5 777266 c.1215G>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304848 p.Asn640Asp missense_variant 0.1
fbiC 1304969 p.Leu680Pro missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473901 n.244G>C non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
inhA 1674349 p.Ile50Val missense_variant 0.11
inhA 1674353 p.Thr51Ile missense_variant 0.11
inhA 1674568 p.Ser123Pro missense_variant 0.12
rpsA 1834937 p.Ser466Cys missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102111 p.Ile311Thr missense_variant 0.11
ndh 2103011 p.Pro11Gln missense_variant 0.13
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.19
PPE35 2169602 c.1011C>A synonymous_variant 0.17
PPE35 2169890 c.723C>T synonymous_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290146 c.-905G>T upstream_gene_variant 0.15
kasA 2519264 p.Val384Ile missense_variant 0.15
folC 2746654 c.945C>T synonymous_variant 0.17
Rv2752c 3064532 p.Thr554Ala missense_variant 0.14
fbiD 3339702 c.585G>C synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642596 c.1062C>A synonymous_variant 0.12
alr 3841041 p.Asp127Gly missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.25
rpoA 3877869 p.Lys213Asn missense_variant 0.14
rpoA 3878481 c.26dupT frameshift_variant 0.15
rpoA 3878487 c.21C>A synonymous_variant 0.15
clpC1 4039018 p.Ser563Ala missense_variant 0.4
clpC1 4039022 c.1683A>G synonymous_variant 0.4
clpC1 4040057 c.648C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.47
embB 4246548 p.Pro12Gln missense_variant 0.58
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4246563 p.Leu17Trp missense_variant 0.38
embB 4246567 c.54G>T synonymous_variant 0.43
embB 4247024 p.Pro171Ala missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.18
aftB 4268691 p.Phe49Tyr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407664 p.Ala180Glu missense_variant 0.13