TB-Profiler result

Run: ERR11043873
Summary

Run ID: ERR11043873

Sample name:

Date: 31-03-2023 11:42:44

Number of reads: 432237

Percentage reads mapped: 99.57

Strain: lineage3.1.1

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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
gyrB 6173 p.Glu312Gln missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575839 c.492G>A synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761398 p.Asp531Gly missense_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766364 p.Ala999Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776031 p.Gly817Glu missense_variant 0.25
mmpL5 776083 p.Ala800Thr missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776908 p.Gln525* stop_gained 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303947 c.1017T>C synonymous_variant 0.14
embR 1416216 p.Phe378Leu missense_variant 0.11
embR 1416580 c.768T>C synonymous_variant 0.13
atpE 1460878 c.-167C>T upstream_gene_variant 0.17
atpE 1461160 p.Val39Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473962 n.305T>A non_coding_transcript_exon_variant 0.11
inhA 1674670 p.Ala157Thr missense_variant 0.12
rpsA 1833551 p.Pro4Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168896 p.Gly573Cys missense_variant 0.23
PPE35 2168926 p.Val563Leu missense_variant 0.18
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170545 p.Pro23Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714896 p.Phe146Ser missense_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064844 p.Asp450Asn missense_variant 0.22
Rv2752c 3067039 c.-848T>A upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841394 c.26delG frameshift_variant 0.14
clpC1 4039830 p.Leu292Ser missense_variant 0.13
panD 4044079 p.Val68Gly missense_variant 0.12
embC 4239705 c.-158T>A upstream_gene_variant 0.17
embC 4240133 p.Ala91Thr missense_variant 0.15
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242834 p.Phe991Ser missense_variant 0.11
embC 4242963 p.Gly1034Asp missense_variant 0.14
whiB6 4338470 p.Asn18Asp missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408345 c.-143C>T upstream_gene_variant 1.0