TB-Profiler result

Run: ERR2229523
Summary

Run ID: ERR2229523

Sample name:

Date: 31-03-2023 17:17:20

Number of reads: 954346

Percentage reads mapped: 99.18

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 7837 p.Gly179Ala missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.47
rpoB 761168 c.1362C>A synonymous_variant 0.33
rpoC 762767 c.-603G>A upstream_gene_variant 0.18
rpoC 763509 p.Phe47Tyr missense_variant 0.14
rpoC 763886 p.Arg173Trp missense_variant 0.13
rpoC 765703 c.2336delA frameshift_variant 0.13
rpoC 766981 c.3612T>G synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776255 c.2226C>A synonymous_variant 0.12
mmpL5 776460 p.Ala674Glu missense_variant 0.12
mmpL5 776739 p.Ile581Thr missense_variant 0.11
mmpL5 777071 p.Lys470Asn missense_variant 0.15
mmpL5 777569 c.912C>T synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800614 c.-195C>T upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406498 p.Leu281Phe missense_variant 0.13
Rv1258c 1407190 p.Thr51Ala missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.18
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.18
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.18
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.18
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.17
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.18
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.2
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.25
rrs 1472837 n.992C>G non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476202 n.2545G>T non_coding_transcript_exon_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
inhA 1673832 c.-370A>G upstream_gene_variant 0.17
rpsA 1834282 c.741C>T synonymous_variant 0.13
rpsA 1834490 p.Ile317Val missense_variant 0.15
rpsA 1834607 p.Arg356Cys missense_variant 0.25
rpsA 1834621 p.Leu360Phe missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918289 p.Gln117Arg missense_variant 0.11
ndh 2101693 c.1350C>T synonymous_variant 0.12
katG 2153960 p.Pro718Ala missense_variant 0.22
katG 2156269 c.-158C>T upstream_gene_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170147 p.Ser156Ala missense_variant 0.18
PPE35 2170157 p.Ala152Ser missense_variant 0.57
Rv1979c 2222812 p.Leu118* stop_gained 0.14
Rv1979c 2222838 p.Leu109Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519013 c.900delG frameshift_variant 0.12
folC 2746660 c.938delT frameshift_variant 0.18
folC 2747661 c.-63G>T upstream_gene_variant 0.13
pepQ 2860284 c.135G>C synonymous_variant 0.11
ribD 2987347 c.512delG frameshift_variant 0.12
Rv2752c 3065543 p.Glu217* stop_gained 0.15
thyX 3067583 c.363C>A synonymous_variant 0.12
thyA 3073896 c.576C>T synonymous_variant 0.12
thyA 3074130 c.342G>A synonymous_variant 0.12
fprA 3474112 p.Val36Phe missense_variant 0.17
fprA 3474279 c.273C>T synonymous_variant 0.14
fprA 3474902 p.Ser299Ile missense_variant 0.18
whiB7 3568428 c.252A>G synonymous_variant 0.33
Rv3236c 3612116 p.Gly334Val missense_variant 0.15
Rv3236c 3612344 p.Arg258Leu missense_variant 0.2
alr 3840672 p.Leu250Pro missense_variant 0.11
alr 3840936 p.Leu162Pro missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.15
clpC1 4039608 p.Tyr366Phe missense_variant 0.11
clpC1 4039654 p.Thr351Ser missense_variant 0.17
clpC1 4039900 c.803_804dupGC frameshift_variant 0.14
clpC1 4040217 p.Gly163Val missense_variant 0.25
embC 4241254 c.1392C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243453 p.Ile74Thr missense_variant 0.13
embA 4245008 c.1776T>C synonymous_variant 0.17
embA 4245038 c.1806C>T synonymous_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.56
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247242 c.729C>T synonymous_variant 0.17
embB 4248779 p.Glu756Lys missense_variant 0.15
aftB 4267022 c.1815T>C synonymous_variant 0.18
aftB 4267919 p.Gln306His missense_variant 0.25
aftB 4267974 p.Ser288* stop_gained 0.13
ethA 4327271 p.Pro68Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407678 c.525G>T synonymous_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0