TB-Profiler result

Run: ERR2229172
Summary

Run ID: ERR2229172

Sample name:

Date: 31-03-2023 16:46:41

Number of reads: 310267

Percentage reads mapped: 99.34

Strain: lineage4

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
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 5289 p.Ile17Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7932 p.Asp211Asn missense_variant 0.33
mmpL5 775981 p.Leu834Met missense_variant 0.29
mmpL5 775987 p.His832Tyr missense_variant 0.33
mmpL5 775990 c.2491C>T synonymous_variant 0.33
mmpL5 778278 p.Ala68Glu missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302897 c.-34G>T upstream_gene_variant 0.4
fbiC 1305311 p.Arg794Gln missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473948 n.291C>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1833425 c.-117C>G upstream_gene_variant 0.33
rpsA 1833436 c.-106C>T upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154924 c.1188C>A synonymous_variant 0.2
PPE35 2167773 p.Gly947Val missense_variant 0.18
PPE35 2167833 p.Leu927Arg missense_variant 0.25
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2168177 c.2436T>A synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169365 p.Ser416Asn missense_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170060 p.Val185Leu missense_variant 0.22
PPE35 2170157 p.Ala152Ser missense_variant 0.2
Rv1979c 2223048 c.117G>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288909 c.333G>A synonymous_variant 0.25
kasA 2518879 c.765A>G synonymous_variant 0.25
kasA 2518882 c.768C>A synonymous_variant 0.29
ribD 2986877 c.39G>T synonymous_variant 0.17
fbiD 3339352 p.Val79Ile missense_variant 0.2
fbiD 3339370 p.Pro85Ser missense_variant 0.29
fprA 3474024 c.18C>T synonymous_variant 0.22
fprA 3474694 p.Leu230Met missense_variant 0.33
Rv3236c 3612791 p.Trp109* stop_gained 0.15
rpoA 3878340 c.168C>A synonymous_variant 0.17
clpC1 4038773 p.Asp644Glu missense_variant 0.5
clpC1 4038776 p.Glu643Asp missense_variant 0.5
clpC1 4038782 c.1923G>C synonymous_variant 0.33
clpC1 4039594 p.Arg371Gly missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040292 p.Val138Glu missense_variant 0.29
clpC1 4040692 p.Phe5Ile missense_variant 0.15
embC 4239705 c.-158T>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243511 c.279G>A synonymous_variant 0.29
embA 4245494 c.2262G>A synonymous_variant 0.4
embA 4246182 p.Ala984Thr missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.71
embB 4246556 p.Ala15Pro missense_variant 0.71
embB 4246563 p.Leu17Trp missense_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247170 c.657G>A synonymous_variant 0.14
aftB 4267111 c.1725delT frameshift_variant 0.2
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
ethR 4327730 p.Phe61Cys missense_variant 0.12
ethA 4328289 c.-816T>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0