TB-Profiler result

Run: ERR2229719
Summary

Run ID: ERR2229719

Sample name:

Date: 31-03-2023 17:28:51

Number of reads: 423930

Percentage reads mapped: 99.29

Strain: lineage4.8

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
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
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 6830 p.Ala531Ser missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7394 c.93T>C synonymous_variant 0.25
gyrA 7668 p.Pro123Thr missense_variant 0.15
fgd1 491292 c.510G>C synonymous_variant 0.33
rpoB 759787 c.-20A>G upstream_gene_variant 0.2
rpoB 761459 c.1653G>A synonymous_variant 0.4
rpoC 763776 p.Ile136Thr missense_variant 0.22
rpoC 766386 p.Pro1006His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775727 c.2754C>G synonymous_variant 0.12
mmpL5 775736 c.2745C>G synonymous_variant 0.12
mmpL5 775741 c.2740C>T synonymous_variant 0.12
mmpL5 775742 c.2739C>T synonymous_variant 0.12
mmpL5 775747 p.Met912Leu missense_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.22
mmpL5 777173 c.1308C>T synonymous_variant 0.22
mmpL5 777176 p.Glu435Asp missense_variant 0.25
mmpL5 778747 c.-267C>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305030 c.2100G>A synonymous_variant 0.25
Rv1258c 1406180 c.1161C>T synonymous_variant 0.29
Rv1258c 1406384 c.957G>T synonymous_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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
inhA 1674374 p.Ala58Asp missense_variant 0.33
rpsA 1834504 c.963G>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.25
PPE35 2167847 c.2766A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170165 p.Ala150Ser missense_variant 0.25
PPE35 2170247 p.Ile122Val missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223305 c.-141G>T upstream_gene_variant 0.33
kasA 2518809 p.Lys232Arg missense_variant 0.33
Rv2752c 3066233 c.-42G>A upstream_gene_variant 0.17
thyX 3068064 c.-119G>T upstream_gene_variant 0.12
alr 3840795 p.Asp209Ala missense_variant 0.22
rpoA 3878362 p.Ala49Glu missense_variant 0.33
clpC1 4040695 p.Arg4* stop_gained 0.22
embC 4239883 c.25dupC frameshift_variant 0.12
embC 4240219 c.357C>G synonymous_variant 0.17
embC 4240648 c.786C>T synonymous_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.42
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
aftB 4267748 p.Phe363Leu missense_variant 0.29
aftB 4268817 p.Trp7Leu missense_variant 0.15
ubiA 4269467 p.Asn123His missense_variant 0.25
aftB 4269471 c.-635C>G upstream_gene_variant 0.22
ethA 4326749 p.Asn242Ser missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0