TB-Profiler result

Run: ERR2229088
Summary

Run ID: ERR2229088

Sample name:

Date: 31-03-2023 16:38:10

Number of reads: 694646

Percentage reads mapped: 99.47

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 7113 p.Thr625Ile missense_variant 0.17
gyrA 7310 p.Asp3Glu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8189 c.888G>A synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoB 761339 c.1533C>A synonymous_variant 0.12
rpoB 762945 c.3142delC frameshift_variant 0.22
rpoB 762988 p.Arg1061Leu missense_variant 0.29
rpoC 764081 p.Glu238* stop_gained 0.17
rpoC 765748 p.Tyr793* stop_gained 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775741 c.2740C>T synonymous_variant 0.17
mmpL5 775747 p.Met912Leu missense_variant 0.17
mmpL5 775748 c.2733T>C synonymous_variant 0.17
mmpL5 776729 c.1752C>T synonymous_variant 0.12
mmpS5 778708 p.Tyr66* stop_gained 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800930 p.Thr41Met missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407169 p.Ala58Thr missense_variant 0.25
embR 1417297 c.51A>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169677 c.936C>G synonymous_variant 0.12
PPE35 2169732 p.Asn294Ser missense_variant 0.15
PPE35 2169882 p.Ser244Asn missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.56
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170447 p.Ser56Ala missense_variant 0.11
PPE35 2170454 c.159C>G synonymous_variant 0.11
PPE35 2170457 c.156G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.27
kasA 2518609 p.Met165Ile missense_variant 0.33
kasA 2519058 p.Thr315Met missense_variant 0.2
eis 2714194 p.Ser380Phe missense_variant 0.17
eis 2715050 p.Gly95Ser missense_variant 0.13
folC 2747566 c.33G>T synonymous_variant 0.22
pepQ 2859436 p.Val328Asp missense_variant 0.14
ribD 2986684 c.-155T>A upstream_gene_variant 0.15
Rv2752c 3065533 p.Pro220Leu missense_variant 0.17
thyX 3067340 c.606G>A synonymous_variant 0.23
thyA 3074043 c.429G>C synonymous_variant 0.25
fprA 3474144 p.Trp46Cys missense_variant 0.17
Rv3236c 3613159 c.-43G>A upstream_gene_variant 0.14
Rv3236c 3613297 c.-182delG upstream_gene_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.11
panD 4043906 p.Glu126Gln missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245577 p.Lys782Arg missense_variant 0.5
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4247936 p.Thr475Ala missense_variant 0.1
embB 4249387 p.Glu958Asp missense_variant 0.15
embB 4249414 c.2901G>T synonymous_variant 0.12
aftB 4267346 c.1491C>T synonymous_variant 0.12
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338637 c.-116A>G upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0