TB-Profiler result

Run: ERR495013
Summary

Run ID: ERR495013

Sample name:

Date: 01-04-2023 21:34:48

Number of reads: 1037823

Percentage reads mapped: 99.54

Strain: lineage4.1.1.3

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
pncA 2288775 p.Leu156Pro missense_variant 0.18 pyrazinamide
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 6216 p.Ser326* stop_gained 0.14
gyrA 7332 p.Ser11Thr missense_variant 0.15
gyrA 7335 p.Leu12Phe missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 0.14
gyrA 8342 c.1041G>A synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759621 c.-186C>T upstream_gene_variant 0.14
rpoB 760274 c.468G>A synonymous_variant 0.18
rpoB 761465 c.1659G>T synonymous_variant 0.14
rpoB 762757 p.Ser984* stop_gained 0.22
rpoC 764937 p.Gln523Leu missense_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765505 c.2136C>T synonymous_variant 0.17
rpoC 766265 p.Leu966Met missense_variant 0.29
rpoC 766845 p.Arg1159His missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776452 p.Gly677Cys missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781458 c.-102C>T upstream_gene_variant 0.13
embR 1416795 p.Gly185Trp missense_variant 0.13
atpE 1461232 p.Ala63Val missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474163 n.506C>T non_coding_transcript_exon_variant 0.33
rrl 1474945 n.1288C>T non_coding_transcript_exon_variant 0.5
rrl 1474947 n.1290G>A non_coding_transcript_exon_variant 0.5
rrl 1475490 n.1833C>T non_coding_transcript_exon_variant 0.18
fabG1 1673506 p.Gly23Lys missense_variant 0.29
fabG1 1674121 p.Asp228Tyr missense_variant 0.25
rpsA 1834220 p.Asp227Tyr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102019 p.Tyr342His missense_variant 0.17
ndh 2103049 c.-7G>A upstream_gene_variant 0.17
katG 2153933 p.Ala727Ser missense_variant 0.43
katG 2155324 p.Ala263Glu missense_variant 0.17
katG 2155898 p.Asp72Asn missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288822 c.420C>T synonymous_variant 0.2
pncA 2288966 c.276G>A synonymous_variant 0.2
ahpC 2726043 c.-150C>T upstream_gene_variant 0.33
folC 2746455 c.1144C>T synonymous_variant 0.2
folC 2746641 p.Gln320* stop_gained 0.33
pepQ 2859654 c.765G>A synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339119 c.4_5delAG frameshift_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568661 p.Pro7Thr missense_variant 0.22
fbiB 3641658 p.Asp42Asn missense_variant 0.15
fbiB 3641807 c.273C>G synonymous_variant 1.0
fbiB 3642112 p.Ala193Val missense_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.25
ddn 3986782 c.-62G>A upstream_gene_variant 0.22
ddn 3986956 p.Gly38Asp missense_variant 0.15
clpC1 4038857 c.1848C>A synonymous_variant 0.5
clpC1 4039134 p.Ala524Val missense_variant 0.14
panD 4044114 c.168C>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245855 p.Gly875Cys missense_variant 0.2
embA 4245868 p.Ser879Phe missense_variant 0.22
embA 4245931 p.Gly900Asp missense_variant 0.25
embB 4245956 c.-558G>T upstream_gene_variant 0.29
embB 4248846 p.Gly778Asp missense_variant 0.17
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326692 p.Arg261Gln missense_variant 0.25
ethR 4327691 p.Asp48Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0