TB-Profiler result

Run: ERR4817427
Summary

Run ID: ERR4817427

Sample name:

Date: 01-04-2023 14:59:17

Number of reads: 862574

Percentage reads mapped: 88.91

Strain: La3

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
La3 M.orygis None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.96 streptomycin
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 5476 p.Asp79Glu missense_variant 0.2
gyrB 5516 p.Ile93Val missense_variant 1.0
gyrB 5788 c.549G>T synonymous_variant 0.15
gyrB 6025 p.Lys262Asn missense_variant 0.12
gyrB 6109 c.870G>A synonymous_variant 1.0
gyrA 6373 c.-929C>A upstream_gene_variant 0.25
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrB 6764 p.Leu509Met missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7589 c.288G>T synonymous_variant 0.15
gyrA 7775 c.474C>T synonymous_variant 1.0
gyrA 8568 p.Glu423Leu missense_variant 0.12
gyrA 8579 c.1278C>T synonymous_variant 0.12
gyrA 8930 c.1629C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9580 p.Gly760Asp missense_variant 0.12
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 1.0
fgd1 491064 c.282A>G synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
mshA 576537 p.Gln397Arg missense_variant 0.12
rpoB 760543 p.Phe246Ser missense_variant 0.11
rpoB 761166 p.Pro454Thr missense_variant 0.14
rpoB 761786 c.1980C>A synonymous_variant 0.29
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.92
rpoB 762873 p.Tyr1023Asn missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765674 p.Glu769Lys missense_variant 0.12
rpoC 765752 p.Asp795Asn missense_variant 0.13
rpoC 765763 c.2394G>T synonymous_variant 0.12
rpoC 766317 p.Met983Thr missense_variant 0.1
rpoC 766443 p.Thr1025Asn missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775735 p.Leu915Ile missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778086 c.394dupG frameshift_variant 1.0
mmpL5 778323 p.Leu53Pro missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781755 p.Tyr66His missense_variant 0.12
rpsL 781862 c.303G>C synonymous_variant 0.1
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303515 c.585G>T synonymous_variant 0.17
fbiC 1303606 c.677_678delAG frameshift_variant 0.15
fbiC 1303739 p.Arg270Leu missense_variant 0.14
embR 1416416 p.Gly311Glu missense_variant 0.14
embR 1416694 c.654C>A synonymous_variant 0.33
atpE 1461271 c.228dupC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.82
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.85
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.85
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.86
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.88
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.95
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.95
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.95
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.86
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.95
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.97
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.94
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.24
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.81
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.81
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.95
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.95
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.99
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.99
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.98
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.87
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.6
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.6
rrl 1473449 n.-209G>A upstream_gene_variant 0.17
rrl 1474157 n.500G>C non_coding_transcript_exon_variant 1.0
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.44
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.44
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.44
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.4
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.55
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.36
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.55
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.75
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.75
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
inhA 1674602 p.Leu134Pro missense_variant 0.12
rpsA 1833632 p.Lys31Glu missense_variant 0.22
rpsA 1834363 c.822G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154700 p.Gln471Arg missense_variant 0.11
katG 2154707 p.Val469Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.94
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156189 c.-78C>A upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169318 p.Phe432Ser missense_variant 0.4
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222643 c.522C>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289405 c.-164A>T upstream_gene_variant 0.12
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
pncA 2290000 c.-759C>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726378 c.186T>A synonymous_variant 1.0
folC 2746391 p.Val403Ala missense_variant 1.0
pepQ 2859612 c.807G>A synonymous_variant 0.13
Rv2752c 3064569 c.1623G>A synonymous_variant 0.15
Rv2752c 3064822 p.Val457Ala missense_variant 0.17
Rv2752c 3065816 p.Val126Phe missense_variant 0.15
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
thyX 3067812 p.Gln45Arg missense_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087444 p.Ala209Ser missense_variant 0.12
Rv3083 3448380 c.-124G>T upstream_gene_variant 0.17
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475113 c.1107G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
whiB7 3568566 c.113delT frameshift_variant 0.13
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
Rv3236c 3613050 p.Ala23Pro missense_variant 0.11
fbiB 3641584 p.Val17Ala missense_variant 1.0
alr 3840758 c.662delA frameshift_variant 0.22
alr 3841384 p.Asp13Tyr missense_variant 0.15
rpoA 3877636 p.Gln291Arg missense_variant 0.1
rpoA 3878479 p.Ser10Tyr missense_variant 0.25
ddn 3987288 p.Cys149Arg missense_variant 0.11
clpC1 4039853 c.852G>A synonymous_variant 1.0
clpC1 4040610 p.His32Arg missense_variant 0.14
clpC1 4040650 p.Glu19* stop_gained 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246694 c.186delG frameshift_variant 0.1
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248511 c.1998C>T synonymous_variant 0.14
embB 4249742 p.Gln1077Lys missense_variant 0.33
aftB 4267344 p.Val498Ala missense_variant 0.12
ubiA 4269277 p.Phe186Ser missense_variant 0.11
aftB 4269339 c.-503C>T upstream_gene_variant 0.13
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327023 p.Phe151Leu missense_variant 0.22
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethR 4328096 p.Leu183Arg missense_variant 0.17
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338376 c.145delG frameshift_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407800 p.Val135Met missense_variant 1.0