TB-Profiler result

Run: ERR1949993
Summary

Run ID: ERR1949993

Sample name:

Date: 31-03-2023 15:36:50

Number of reads: 396095

Percentage reads mapped: 99.35

Strain: lineage4.8

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
lineage4.8 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
pncA 2289156 c.79_85delCTGGCCC frameshift_variant 0.11 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7827 p.Asn176Tyr missense_variant 0.13
mshA 575186 c.-161delG upstream_gene_variant 0.18
rpoB 759792 c.-15C>A upstream_gene_variant 0.38
rpoB 760014 p.Glu70* stop_gained 0.13
rpoB 760043 c.237C>A synonymous_variant 0.11
rpoB 760243 p.Val146Gly missense_variant 0.15
rpoB 760729 p.Tyr308Cys missense_variant 0.14
rpoB 760763 c.957C>T synonymous_variant 0.13
rpoC 762782 c.-588T>G upstream_gene_variant 0.33
rpoC 765907 c.2538G>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777288 p.Val398Gly missense_variant 0.22
mmpL5 778279 p.Ala68Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781857 p.Gly100Ser missense_variant 0.25
rplC 801059 p.Leu84Pro missense_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304143 p.Trp405Gly missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471778 n.-68G>A upstream_gene_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474039 n.382A>T non_coding_transcript_exon_variant 0.17
rrl 1474266 n.609T>A non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>A non_coding_transcript_exon_variant 0.15
rrl 1476607 n.2950C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154156 c.1956A>T synonymous_variant 0.15
katG 2155139 p.Pro325Thr missense_variant 0.15
katG 2156043 c.69G>T synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169789 p.Leu275* stop_gained 0.4
PPE35 2170386 p.Leu76Arg missense_variant 0.33
PPE35 2170518 p.Asp32Val missense_variant 0.22
Rv1979c 2222227 p.Phe313Tyr missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518483 c.369C>T synonymous_variant 0.11
kasA 2519028 p.Ile305Asn missense_variant 0.17
kasA 2519116 c.1002C>T synonymous_variant 0.25
ahpC 2726240 c.48C>T synonymous_variant 0.12
folC 2746804 c.795G>A synonymous_variant 0.13
folC 2747123 p.Ala159Val missense_variant 0.13
folC 2747186 p.Ser138* stop_gained 0.18
pepQ 2859314 p.Leu369Met missense_variant 0.14
pepQ 2859575 p.Ala282Ser missense_variant 0.15
ald 3086709 c.-111G>A upstream_gene_variant 0.11
fprA 3474084 c.78C>A synonymous_variant 0.12
whiB7 3568566 c.114A>C synonymous_variant 0.14
fbiB 3642270 p.Ala246Ser missense_variant 0.22
rpoA 3878245 p.Glu88Gly missense_variant 0.15
ddn 3986782 c.-62G>A upstream_gene_variant 0.12
clpC1 4040377 c.328C>T synonymous_variant 0.14
panD 4044208 p.Ser25Leu missense_variant 0.15
embC 4242153 p.Gly764Asp missense_variant 0.11
embC 4242172 c.2310C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244194 p.Gly321Ala missense_variant 0.17
embB 4247094 p.Gly194Glu missense_variant 0.2
aftB 4268280 p.Arg186Gln missense_variant 0.33
ethA 4328025 c.-552T>C upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1448del transcript_ablation 1.0