TB-Profiler result

Run: ERR403411
Summary

Run ID: ERR403411

Sample name:

Date: 01-04-2023 04:28:29

Number of reads: 3461585

Percentage reads mapped: 99.5

Strain: lineage4.5;lineage3

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
lineage3 East-African-Indian CAS RD750 0.23
lineage4 Euro-American LAM;T;S;X;H None 0.82
lineage4.5 Euro-American H;T RD122 0.81
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.8
gyrA 8042 c.741C>T synonymous_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.17
ccsA 620029 c.139C>T synonymous_variant 0.72
rpoB 759746 c.-61C>T upstream_gene_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.18
mmpL5 777820 c.661C>T synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2170521 p.Trp31* stop_gained 0.86
PPE35 2170568 p.Ile15Met missense_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.2
pncA 2289365 c.-125delC upstream_gene_variant 0.21
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.29
thyA 3073806 c.666C>G synonymous_variant 0.21
thyA 3074585 c.-118_-115delGACT upstream_gene_variant 0.74
ald 3086788 c.-32T>C upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.14
rpoA 3878575 c.-68C>T upstream_gene_variant 0.78
clpC1 4038318 p.Pro796Leu missense_variant 0.73
clpC1 4039481 c.1224T>G synonymous_variant 0.13
clpC1 4039577 c.1128T>C synonymous_variant 0.9
embC 4242075 p.Arg738Gln missense_variant 0.15
embC 4242425 p.Arg855Gly missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246552 c.39T>C synonymous_variant 0.75
embB 4246714 c.201G>T synonymous_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.13