TB-Profiler result

Run: ERR2229369
Summary

Run ID: ERR2229369

Sample name:

Date: 31-03-2023 17:07:27

Number of reads: 924139

Percentage reads mapped: 98.51

Strain: lineage4.8

Drug-resistance: Other

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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
tlyA 1917946 p.Arg3* stop_gained 0.12 capreomycin
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 7103 p.Trp622Arg missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9305 c.2004C>A synonymous_variant 0.18
gyrA 9595 p.Ala765Glu missense_variant 0.13
fgd1 491244 c.462T>C synonymous_variant 0.29
fgd1 491532 c.750G>A synonymous_variant 0.13
mshA 576111 p.Ala255Gly missense_variant 0.33
rpoB 760258 p.Phe151Ser missense_variant 0.12
rpoB 761588 p.Asp594Glu missense_variant 0.13
rpoB 762580 p.Ile925Asn missense_variant 0.14
rpoC 763786 c.417C>A synonymous_variant 0.22
rpoC 765031 p.Glu554Asp missense_variant 0.17
rpoC 765070 c.1701G>T synonymous_variant 0.17
rpoC 765084 p.Arg572Leu missense_variant 0.17
rpoC 766520 p.Gly1051Cys missense_variant 0.2
rpoC 767207 p.Ala1280Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775883 p.Ile866Leu missense_variant 0.25
mmpL5 776018 c.2463G>T synonymous_variant 0.43
mmpL5 776108 p.Met791Ile missense_variant 0.4
mmpL5 776194 p.Ala763Ser missense_variant 0.14
mmpL5 777122 c.1359C>T synonymous_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 778615 c.-135G>A upstream_gene_variant 0.18
mmpL5 778949 c.-469G>T upstream_gene_variant 0.15
mmpL5 778965 c.-485G>T upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781594 p.Arg12His missense_variant 0.14
fbiC 1302756 c.-175G>T upstream_gene_variant 0.14
fbiC 1302771 c.-160G>T upstream_gene_variant 0.12
fbiC 1302797 c.-134C>A upstream_gene_variant 0.12
fbiC 1302799 c.-132T>C upstream_gene_variant 0.11
fbiC 1302812 c.-119G>T upstream_gene_variant 0.16
fbiC 1303500 p.His190Gln missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304301 c.1371C>T synonymous_variant 0.18
fbiC 1305366 p.Met812Ile missense_variant 0.14
Rv1258c 1406579 p.His254Gln missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.25
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.14
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472764 n.919G>T non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.3
rrs 1472840 n.995A>T non_coding_transcript_exon_variant 0.22
rrs 1472844 n.999C>T non_coding_transcript_exon_variant 0.22
rrl 1473833 n.176G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.29
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.25
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 0.25
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.25
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.25
rrl 1475728 n.2071C>A non_coding_transcript_exon_variant 0.18
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.24
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.27
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.19
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.24
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.14
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.14
rrl 1476255 n.2598A>G non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476267 n.2610G>A non_coding_transcript_exon_variant 0.14
rrl 1476276 n.2619C>T non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25
fabG1 1673219 c.-221C>A upstream_gene_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1833684 p.Arg48Gln missense_variant 0.15
rpsA 1834665 p.Pro375Leu missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917991 c.52C>A synonymous_variant 0.17
tlyA 1918063 p.Pro42Ala missense_variant 0.17
ndh 2102292 p.Asp251Asn missense_variant 0.4
ndh 2102724 p.Thr107Ala missense_variant 0.18
ndh 2102832 p.Pro71Thr missense_variant 0.33
katG 2154138 p.Phe658Leu missense_variant 0.31
katG 2154151 p.Thr654Asn missense_variant 0.15
katG 2154312 p.Lys600Asn missense_variant 0.18
katG 2154629 p.Gly495Cys missense_variant 0.17
katG 2154807 c.1305C>A synonymous_variant 0.18
katG 2155008 c.1104C>T synonymous_variant 0.13
katG 2155191 c.921A>C synonymous_variant 0.2
katG 2155322 p.Ala264Ser missense_variant 0.25
PPE35 2167833 p.Leu927Arg missense_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.37
PPE35 2167967 c.2646A>C synonymous_variant 0.37
PPE35 2168140 p.Ala825Thr missense_variant 0.18
PPE35 2168143 p.Phe824Leu missense_variant 0.2
PPE35 2168150 c.2463T>C synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168921 c.1692G>T synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.25
PPE35 2169351 p.Ala421Gly missense_variant 0.13
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.57
Rv1979c 2222074 p.Pro364Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289238 c.4C>A synonymous_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.25
kasA 2519338 c.1224T>C synonymous_variant 0.29
ahpC 2726450 c.258G>A synonymous_variant 0.12
folC 2747661 c.-63G>T upstream_gene_variant 0.25
pepQ 2859343 p.Pro359Gln missense_variant 0.14
pepQ 2859547 p.Gly291Val missense_variant 0.22
pepQ 2860311 p.Phe36Leu missense_variant 0.17
ribD 2987040 p.Arg68Gly missense_variant 0.2
thyX 3067609 p.Asp113Tyr missense_variant 0.29
thyX 3067613 p.Glu111Asp missense_variant 0.33
thyX 3068011 c.-66C>T upstream_gene_variant 0.22
thyX 3068015 c.-70T>G upstream_gene_variant 0.22
ald 3086737 c.-83T>A upstream_gene_variant 0.18
ald 3087822 p.Ser335Ala missense_variant 0.22
Rv3083 3448406 c.-98G>T upstream_gene_variant 0.2
fprA 3474379 p.Ala125Ser missense_variant 0.22
fprA 3474441 c.435G>A synonymous_variant 0.17
Rv3236c 3611966 p.Ser384* stop_gained 0.29
Rv3236c 3611978 p.Ala380Asp missense_variant 0.29
Rv3236c 3613310 c.-194T>A upstream_gene_variant 0.13
fbiA 3640358 c.-185C>A upstream_gene_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3878187 c.321C>A synonymous_variant 0.14
clpC1 4038281 p.Asp808Glu missense_variant 0.2
clpC1 4038432 p.Leu758Pro missense_variant 0.2
clpC1 4038928 c.1777C>A synonymous_variant 0.22
clpC1 4038962 p.Asp581Glu missense_variant 0.22
clpC1 4039018 p.Ser563Ala missense_variant 1.0
clpC1 4039022 c.1683A>G synonymous_variant 1.0
clpC1 4039031 c.1674T>C synonymous_variant 0.67
clpC1 4039161 c.1543delC frameshift_variant 0.18
clpC1 4039169 p.Glu512Asp missense_variant 0.11
embC 4240252 c.390G>T synonymous_variant 0.22
embA 4242274 c.-959G>T upstream_gene_variant 0.2
embA 4242364 c.-869C>A upstream_gene_variant 0.33
embC 4242393 p.Asp844Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243862 c.630C>A synonymous_variant 0.15
embA 4243908 c.676C>A synonymous_variant 0.15
embA 4244070 p.Val280Ile missense_variant 0.2
embA 4244378 c.1148delC frameshift_variant 0.18
embA 4244957 c.1725C>T synonymous_variant 0.33
embA 4244958 p.Ala576Ser missense_variant 0.33
embA 4245146 c.1914G>A synonymous_variant 0.18
embB 4245824 c.-690G>T upstream_gene_variant 0.29
embB 4246088 c.-426A>G upstream_gene_variant 0.17
embA 4246220 p.His996Gln missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.41
embB 4246548 p.Pro12Gln missense_variant 0.59
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54_55insT frameshift_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247119 c.606C>T synonymous_variant 0.33
embB 4247610 p.Ser366Trp missense_variant 0.1
aftB 4267731 p.Arg369Leu missense_variant 0.13
aftB 4269471 c.-635C>A upstream_gene_variant 0.16
aftB 4269531 c.-695G>T upstream_gene_variant 0.14
ethA 4326297 p.Leu393Met missense_variant 0.15
ethR 4327099 c.-450C>A upstream_gene_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