TB-Profiler result

Run: ERR2229404
Summary

Run ID: ERR2229404

Sample name:

Date: 31-03-2023 17:10:12

Number of reads: 911632

Percentage reads mapped: 98.62

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
fgd1 491140 p.Gly120Cys missense_variant 0.14
fgd1 491144 p.Ala121Gly missense_variant 0.14
fgd1 491315 p.Gly178Val missense_variant 0.33
fgd1 491326 p.Ala182Ser missense_variant 0.25
fgd1 491379 c.597C>A synonymous_variant 0.25
mshA 575204 c.-144C>T upstream_gene_variant 0.5
mshA 576377 p.Asp344Tyr missense_variant 0.25
ccsA 620210 p.Trp107Leu missense_variant 0.13
ccsA 620565 c.675G>A synonymous_variant 0.13
rpoB 761804 p.Met666Ile missense_variant 0.18
rpoC 765559 c.2190G>T synonymous_variant 0.12
rpoC 767261 p.Gly1298Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777162 c.1318dupC frameshift_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801427 p.Met207Val missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303834 p.Ala302Thr missense_variant 0.14
Rv1258c 1406137 p.Glu402Lys missense_variant 0.17
Rv1258c 1406457 p.Val295Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472358 n.513C>A non_coding_transcript_exon_variant 0.18
rrl 1473632 n.-26G>T upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474885 n.1228G>T non_coding_transcript_exon_variant 0.14
rrl 1476567 n.2910C>A non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
inhA 1673892 c.-310C>A upstream_gene_variant 0.18
fabG1 1673958 p.Lys173Asn missense_variant 0.15
inhA 1674528 c.327C>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103109 c.-67C>T upstream_gene_variant 0.12
katG 2155802 c.310C>A synonymous_variant 0.13
katG 2156164 c.-53G>T upstream_gene_variant 0.14
PPE35 2167706 c.2907T>C synonymous_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.16
PPE35 2167967 c.2646A>C synonymous_variant 0.16
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169337 p.Asp426His missense_variant 0.14
PPE35 2169602 c.1011C>A synonymous_variant 0.19
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2221743 c.1422T>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518823 p.Phe237Val missense_variant 0.18
kasA 2519055 p.Ala314Glu missense_variant 0.2
eis 2714903 c.430C>A synonymous_variant 0.15
pepQ 2859608 p.Arg271Trp missense_variant 0.18
pepQ 2859832 p.Ala196Val missense_variant 0.15
pepQ 2860318 p.Ser34* stop_gained 0.13
pepQ 2860607 c.-189A>T upstream_gene_variant 0.2
thyA 3074438 p.Leu12Phe missense_variant 0.18
thyA 3074567 c.-96C>A upstream_gene_variant 0.13
ald 3087165 p.Ala116Ser missense_variant 0.17
ald 3087883 p.Val355Glu missense_variant 0.17
fbiD 3339585 c.468C>A synonymous_variant 0.2
fprA 3474141 c.135C>T synonymous_variant 0.14
fprA 3474144 p.Trp46Cys missense_variant 0.15
fprA 3474441 c.435G>T synonymous_variant 0.12
fprA 3474994 p.Pro330Thr missense_variant 0.18
Rv3236c 3612749 p.Gly123Ala missense_variant 0.17
fbiA 3640373 c.-170C>A upstream_gene_variant 0.13
fbiA 3640486 c.-57G>T upstream_gene_variant 0.18
fbiA 3641514 p.Cys324* stop_gained 0.19
fbiB 3641907 p.Pro125Thr missense_variant 0.15
fbiB 3641947 p.Glu138Gly missense_variant 0.14
alr 3841361 c.60G>A synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.25
ddn 3986767 c.-77C>G upstream_gene_variant 0.15
ddn 3987048 p.Asp69His missense_variant 0.11
clpC1 4038342 p.Lys788Arg missense_variant 0.11
clpC1 4040399 p.Tyr102* stop_gained 0.12
clpC1 4040512 p.Glu65* stop_gained 0.17
panD 4044090 c.192C>A synonymous_variant 0.33
embC 4239779 c.-84C>A upstream_gene_variant 0.14
embC 4241900 p.His680Tyr missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.2
embA 4243458 p.Cys76Ser missense_variant 0.25
embA 4243933 p.Arg234His missense_variant 0.15
embA 4245392 c.2160G>A synonymous_variant 0.17
embA 4245433 p.Ala734Glu missense_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.44
embB 4246548 p.Pro12Gln missense_variant 0.65
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.36
embB 4249168 c.2655C>G synonymous_variant 0.2
aftB 4269543 c.-707G>T upstream_gene_variant 0.12
ethA 4327031 p.Ser148Leu missense_variant 0.12
ethR 4327636 p.Leu30Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408057 p.Leu49Gln missense_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0