TB-Profiler result

Run: ERR2229294
Summary

Run ID: ERR2229294

Sample name:

Date: 31-03-2023 16:58:06

Number of reads: 1050797

Percentage reads mapped: 99.1

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
tlyA 1918255 c.319delC frameshift_variant 0.13 capreomycin
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 9398 c.2097T>C synonymous_variant 0.11
fgd1 491767 p.Ala329Pro missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.44
rpoC 764059 c.693delC frameshift_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775717 c.2762_2763delTC frameshift_variant 0.11
mmpL5 775736 c.2745C>G synonymous_variant 0.17
mmpL5 775741 c.2740C>T synonymous_variant 0.16
mmpL5 776018 c.2463G>C synonymous_variant 0.12
mmpL5 776021 c.2460G>C synonymous_variant 0.12
mmpL5 777128 c.1353A>G synonymous_variant 0.11
mmpL5 777176 p.Glu435Asp missense_variant 0.17
mmpL5 777179 c.1302G>C synonymous_variant 0.13
mmpS5 778752 p.Asp52His missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304805 c.1878dupC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474145 n.488T>A non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102080 c.963C>T synonymous_variant 0.13
ndh 2102178 p.Leu289Phe missense_variant 0.15
ndh 2102214 p.Ser277Thr missense_variant 0.4
PPE35 2167745 p.Thr956Arg missense_variant 0.16
PPE35 2167833 p.Leu927Arg missense_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.23
PPE35 2170147 p.Ser156Ala missense_variant 0.18
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2223063 c.102A>G synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.15
folC 2747167 p.Lys144Asn missense_variant 0.13
ribD 2987226 p.Met130Val missense_variant 0.13
whiB7 3568714 c.-35A>C upstream_gene_variant 0.2
Rv3236c 3613072 p.Leu15Phe missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.23
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3878687 c.-180A>G upstream_gene_variant 0.12
clpC1 4038190 p.Ser839Arg missense_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.14
panD 4043940 c.342G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4249177 c.2664G>T synonymous_variant 0.12
ethA 4326930 p.Gly182Cys missense_variant 0.12
ethA 4327062 p.Ser138Gly missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0