TB-Profiler result

Run: ERR2229159
Summary

Run ID: ERR2229159

Sample name:

Date: 31-03-2023 16:46:36

Number of reads: 1125506

Percentage reads mapped: 99.26

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 0.99
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 7434 p.Arg45Ser missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576280 c.933A>G synonymous_variant 0.25
mshA 576628 c.1281G>A synonymous_variant 0.13
ccsA 620594 p.Phe235Tyr missense_variant 0.14
ccsA 620596 p.Ala236Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776031 p.Gly817Val missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
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 0.14
inhA 1674195 c.-7G>T upstream_gene_variant 0.12
inhA 1674981 c.780C>T synonymous_variant 0.15
rpsA 1834714 c.1173C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101918 p.Arg375Ser missense_variant 0.17
ndh 2102086 c.957G>T synonymous_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.14
katG 2155625 p.Asp163Tyr missense_variant 0.12
katG 2155716 c.396T>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170540 c.73C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.19
eis 2715034 p.Met100Arg missense_variant 0.11
folC 2747198 p.Ile134Asn missense_variant 0.17
folC 2747286 p.Val105Leu missense_variant 0.14
pepQ 2859450 c.969C>A synonymous_variant 0.13
thyA 3074580 c.-109T>C upstream_gene_variant 0.2
Rv3083 3448488 c.-16C>A upstream_gene_variant 0.18
Rv3236c 3612302 p.Thr272Lys missense_variant 0.25
fbiA 3640669 p.Ala43Pro missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.13
clpC1 4038576 p.Leu710Pro missense_variant 0.12
clpC1 4038762 p.Thr648Ile missense_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.11
clpC1 4038873 p.Thr611Ile missense_variant 0.17
clpC1 4039344 p.Glu454Gly missense_variant 0.13
clpC1 4039420 p.Ala429Thr missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.17
clpC1 4040265 p.Gly147Val missense_variant 0.12
panD 4044323 c.-42G>T upstream_gene_variant 0.12
embC 4241406 p.Glu515Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242907 c.-326G>A upstream_gene_variant 0.12
embA 4245697 p.Asn822Ser missense_variant 0.2
embA 4246394 p.Trp1054Cys missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246645 c.134_135insCCC disruptive_inframe_insertion 0.14
ethR 4327633 p.Ile29Phe missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0