TB-Profiler result

Run: ERR2229578
Summary

Run ID: ERR2229578

Sample name:

Date: 31-03-2023 17:19:48

Number of reads: 552856

Percentage reads mapped: 98.5

Strain: lineage4

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
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 5521 c.282G>T synonymous_variant 0.17
gyrB 5850 p.Leu204Pro missense_variant 0.2
gyrB 6351 p.Thr371Asn missense_variant 0.22
gyrA 6565 c.-737G>A upstream_gene_variant 0.2
gyrB 7127 p.Val630Leu missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9423 p.Asp708Asn missense_variant 0.2
gyrA 9808 p.Thr836Lys missense_variant 0.18
fgd1 490643 c.-140C>A upstream_gene_variant 0.17
fgd1 491112 c.330G>T synonymous_variant 0.25
fgd1 491264 p.Ser161Leu missense_variant 0.5
mshA 575746 c.399C>A synonymous_variant 0.29
mshA 576100 p.Asp251Glu missense_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576786 p.Ala480Glu missense_variant 0.33
ccsA 620634 c.744C>A synonymous_variant 0.17
ccsA 620661 c.771C>A synonymous_variant 0.2
rpoB 759683 c.-124T>G upstream_gene_variant 0.17
rpoB 759816 p.Ser4Thr missense_variant 0.15
rpoB 759967 p.Ser54* stop_gained 0.4
rpoB 761095 p.Leu430Gln missense_variant 0.15
rpoB 761333 c.1527G>T synonymous_variant 0.2
rpoB 761790 p.Arg662Cys missense_variant 0.2
rpoB 762039 p.His745Tyr missense_variant 0.14
rpoB 762835 p.Gly1010Val missense_variant 0.22
rpoB 762892 p.His1029Arg missense_variant 0.14
rpoB 762952 p.Gln1049Arg missense_variant 0.25
rpoC 763726 p.Asp119Glu missense_variant 0.14
rpoC 764175 p.Asp269Val missense_variant 0.4
rpoC 764825 p.Val486Leu missense_variant 0.12
rpoC 765900 p.Leu844Pro missense_variant 0.18
rpoC 766440 p.Ile1024Asn missense_variant 0.29
rpoC 766618 c.3249G>T synonymous_variant 0.5
rpoC 766966 p.Glu1199Asp missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Val missense_variant 0.33
mmpL5 775817 c.2664T>C synonymous_variant 0.33
mmpL5 775820 c.2661G>A synonymous_variant 0.4
mmpL5 778003 p.Ser160Thr missense_variant 0.4
rpsL 781365 c.-195T>C upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781442 c.-118C>T upstream_gene_variant 0.17
fbiC 1302819 c.-112G>T upstream_gene_variant 0.17
fbiC 1303526 p.Ser199* stop_gained 0.29
fbiC 1303551 c.621G>T synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304569 p.Val547Leu missense_variant 0.4
fbiC 1304665 p.Leu579Met missense_variant 0.15
fbiC 1304682 c.1752C>T synonymous_variant 0.17
fbiC 1305150 c.2220C>G synonymous_variant 0.15
Rv1258c 1406702 c.639C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475706 n.2049A>G non_coding_transcript_exon_variant 0.29
rrl 1475982 n.2325G>A non_coding_transcript_exon_variant 0.29
rrl 1476168 n.2511A>G non_coding_transcript_exon_variant 0.14
rrl 1476521 n.2864C>A non_coding_transcript_exon_variant 0.67
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
fabG1 1673426 c.-14G>T upstream_gene_variant 0.15
inhA 1674750 c.549T>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.2
ndh 2102745 p.Val100Ile missense_variant 0.4
katG 2154090 p.Asp674Glu missense_variant 0.2
katG 2155273 p.Pro280Leu missense_variant 0.22
katG 2155928 p.Phe62Leu missense_variant 0.33
katG 2156551 c.-440C>A upstream_gene_variant 0.12
PPE35 2167784 c.2829C>T synonymous_variant 0.29
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168140 p.Ala825Thr missense_variant 0.22
PPE35 2168143 p.Phe824Leu missense_variant 0.18
PPE35 2168150 c.2463T>C synonymous_variant 0.15
PPE35 2168463 p.Pro717His missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.33
PPE35 2169063 p.Met517Arg missense_variant 0.4
PPE35 2169322 c.1291T>C synonymous_variant 0.14
PPE35 2169326 c.1287C>T synonymous_variant 0.14
PPE35 2169337 p.Asp426His missense_variant 0.18
PPE35 2169377 p.Phe412Leu missense_variant 0.12
PPE35 2169884 c.729T>C synonymous_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.38
PPE35 2170147 p.Ser156Ala missense_variant 0.44
PPE35 2170157 p.Ala152Ser missense_variant 0.27
PPE35 2170403 c.210C>G synonymous_variant 0.25
PPE35 2170406 c.207A>G synonymous_variant 0.22
PPE35 2170436 c.177T>G synonymous_variant 0.17
Rv1979c 2221948 p.Ala406Asp missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.38
kasA 2518609 p.Met165Ile missense_variant 0.29
kasA 2518624 c.510C>A synonymous_variant 0.33
kasA 2518805 p.Asp231Asn missense_variant 0.5
eis 2714682 c.651A>G synonymous_variant 0.14
folC 2746204 c.1395G>T synonymous_variant 0.4
folC 2747715 c.-117G>T upstream_gene_variant 0.2
pepQ 2859363 c.1056T>C synonymous_variant 0.17
pepQ 2860522 c.-104G>C upstream_gene_variant 0.33
Rv2752c 3065651 p.Arg181Cys missense_variant 0.12
Rv2752c 3065898 c.294C>A synonymous_variant 0.2
thyX 3067791 p.Pro52His missense_variant 0.22
ald 3086648 c.-172_-171delTCinsAA upstream_gene_variant 0.22
ald 3086890 p.Ala24Val missense_variant 0.25
ald 3087242 c.424delG frameshift_variant 0.17
fbiD 3339543 c.426C>T synonymous_variant 0.22
fprA 3474108 p.Met34Ile missense_variant 0.25
fprA 3474160 p.Gly52Arg missense_variant 0.22
fprA 3474844 p.Gly280Cys missense_variant 0.67
Rv3236c 3613158 c.-42G>T upstream_gene_variant 0.29
fbiA 3641300 p.Arg253His missense_variant 0.13
clpC1 4038478 p.Lys743Glu missense_variant 0.17
clpC1 4038977 c.1728G>T synonymous_variant 0.2
clpC1 4039519 p.Pro396Ser missense_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.2
clpC1 4039530 p.Asp392Ala missense_variant 0.2
clpC1 4039556 c.1149G>A synonymous_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.25
clpC1 4040057 c.648C>T synonymous_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.2
panD 4044332 c.-51C>A upstream_gene_variant 0.67
panD 4044376 c.-95C>A upstream_gene_variant 0.25
panD 4044380 c.-99C>G upstream_gene_variant 0.25
embC 4240714 p.Trp284Cys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244324 c.1092T>C synonymous_variant 0.4
embA 4244553 p.Gln441Lys missense_variant 0.5
embA 4245468 p.Asn746Tyr missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247070 p.Val186Asp missense_variant 0.33
embB 4247239 c.726G>A synonymous_variant 0.67
embB 4248442 c.1929C>A synonymous_variant 0.13
aftB 4267879 p.Val320Met missense_variant 0.17
ethA 4326487 c.987A>G synonymous_variant 0.14
ethA 4326789 p.Leu229Val missense_variant 0.14
ethA 4326833 p.Ser214Trp missense_variant 0.13
ethA 4327540 c.-67C>A upstream_gene_variant 0.14
ethA 4327547 c.-74C>T upstream_gene_variant 0.13
ethA 4328327 c.-855C>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408280 c.-78G>A upstream_gene_variant 0.17