TB-Profiler result

Run: ERR2229335
Summary

Run ID: ERR2229335

Sample name:

Date: 31-03-2023 17:03:29

Number of reads: 1358064

Percentage reads mapped: 98.9

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 6001 c.762G>T synonymous_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576111 p.Ala255Gly missense_variant 0.14
mshA 576532 c.1185C>T synonymous_variant 0.13
ccsA 620592 c.702C>A synonymous_variant 0.12
rpoB 760437 p.Asp211Asn missense_variant 0.22
rpoB 760445 c.639C>A synonymous_variant 0.29
rpoB 762531 c.2727delT frameshift_variant 0.14
rpoC 764535 p.Arg389Pro missense_variant 0.21
rpoC 766822 c.3453C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776049 p.Ser811* stop_gained 0.18
mmpR5 778139 c.-851G>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 1304043 p.Trp371Cys missense_variant 0.15
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.14
Rv1258c 1406946 p.Ala132Gly missense_variant 0.14
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.14
embR 1416916 c.432A>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
inhA 1674770 p.Ala190Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.23
ndh 2102202 p.Ser281Ala missense_variant 0.15
katG 2153970 p.Asp714Glu missense_variant 0.13
katG 2155139 p.Pro325Thr missense_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169447 p.Phe389Ser missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519346 p.Leu411Pro missense_variant 0.12
Rv2752c 3066187 c.4delG frameshift_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.19
thyX 3067877 c.69G>A synonymous_variant 0.13
thyA 3074451 c.21G>C synonymous_variant 0.22
fprA 3474011 p.Arg2His missense_variant 0.12
whiB7 3568534 p.Arg49Met missense_variant 0.2
Rv3236c 3612589 c.528C>G synonymous_variant 0.2
fbiB 3642796 p.Leu421* stop_gained 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.2
clpC1 4039508 c.1197G>C synonymous_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.12
clpC1 4040331 p.Val125Gly missense_variant 0.17
embC 4239835 c.-28C>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244564 c.1332G>T synonymous_variant 0.11
embA 4245268 p.Asn679Ser missense_variant 0.12
embA 4245974 p.Ile914Met missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246567 c.54_55insT frameshift_variant 0.5
aftB 4267895 p.Phe314Leu missense_variant 0.21
ubiA 4269125 p.Ala237Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407858 c.345G>T synonymous_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0