TB-Profiler result

Run: ERR2229572
Summary

Run ID: ERR2229572

Sample name:

Date: 31-03-2023 17:19:31

Number of reads: 1084955

Percentage reads mapped: 99.05

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8090 c.789C>G synonymous_variant 0.1
mshA 576100 p.Asp251Glu missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.14
mshA 576111 p.Ala255Gly missense_variant 0.17
ccsA 619955 p.Val22Ala missense_variant 0.13
rpoC 765670 c.2301C>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776043 p.Gly813Val missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 0.95
Rv1258c 1406638 p.Val235Phe missense_variant 0.17
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 0.23
inhA 1673988 c.-214G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102913 p.Ala44Ser missense_variant 0.2
katG 2155996 p.Trp39* stop_gained 0.12
PPE35 2167997 c.2616G>C synonymous_variant 0.18
PPE35 2168145 p.Pro823Leu missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169790 p.Leu275Met missense_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170157 p.Ala152Ser missense_variant 0.14
PPE35 2170176 p.Leu146Gln missense_variant 0.13
PPE35 2170178 c.435T>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289969 c.-728G>A upstream_gene_variant 0.14
kasA 2518612 c.498C>G synonymous_variant 0.17
kasA 2518618 c.504G>A synonymous_variant 0.18
kasA 2518624 c.510C>G synonymous_variant 0.21
kasA 2518628 p.Ser172Pro missense_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.17
kasA 2519071 c.957C>T synonymous_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.18
kasA 2519143 c.1029G>C synonymous_variant 0.18
folC 2747197 c.402C>T synonymous_variant 0.12
ribD 2987042 c.204A>T synonymous_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474182 p.Lys59Thr missense_variant 0.15
fprA 3475042 p.Gly346Ser missense_variant 0.12
fbiB 3642414 p.Pro294Thr missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.2
clpC1 4039682 c.1023C>T synonymous_variant 0.12
clpC1 4039730 c.975C>G synonymous_variant 0.29
embC 4240205 p.Lys115Glu missense_variant 0.11
embC 4240463 p.Phe201Val missense_variant 0.14
embC 4241807 p.Pro649Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243440 p.Leu70Val missense_variant 0.13
embA 4246018 p.Leu929Arg missense_variant 0.12
embA 4246122 p.Leu964Met missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.19
embB 4246567 c.54_55insT frameshift_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.11
embB 4247028 p.Leu172Gln missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0