TB-Profiler result

Run: ERR4822066
Summary

Run ID: ERR4822066

Sample name:

Date: 01-04-2023 17:36:53

Number of reads: 523150

Percentage reads mapped: 92.33

Strain: lineage4.1.2.1

Drug-resistance: HR-TB

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 0.85 streptomycin
katG 2154347 p.Pro589Thr missense_variant 0.18 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620861 p.Gly324Asp missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764480 p.Lys371Glu missense_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765514 p.Lys715Asn missense_variant 0.25
rpoC 766965 p.Glu1199Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776453 p.Met676Ile missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800872 p.Arg22* stop_gained 0.15
fbiC 1305055 p.Met709Leu missense_variant 0.2
Rv1258c 1406458 p.Val295Ile missense_variant 0.18
Rv1258c 1406650 p.Ile231Val missense_variant 0.14
embR 1417219 c.129C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.8
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.8
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.8
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.8
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.79
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.86
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.87
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.82
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.79
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.79
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.89
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.87
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.87
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.88
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.88
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.93
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.67
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.67
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.67
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.67
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.67
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.6
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.5
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.4
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.4
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.5
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.75
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.67
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.67
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.57
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.91
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.91
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.91
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.91
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.8
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
fabG1 1673923 p.Gly162Cys missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918454 p.Ser172Leu missense_variant 0.12
ndh 2102322 p.Val241Met missense_variant 0.29
ndh 2103078 c.-36C>T upstream_gene_variant 0.22
PPE35 2169151 p.Pro488Ser missense_variant 0.14
Rv1979c 2222126 p.Asp347Asn missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-157delG upstream_gene_variant 0.18
pncA 2289519 c.-278T>G upstream_gene_variant 0.33
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518840 c.726C>T synonymous_variant 0.14
eis 2715293 p.Pro14Ala missense_variant 0.25
folC 2747603 c.-5C>A upstream_gene_variant 0.13
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2987037 c.200delA frameshift_variant 0.17
thyX 3067721 c.225T>C synonymous_variant 0.29
thyX 3067727 c.219A>C synonymous_variant 0.22
thyX 3067742 c.204A>G synonymous_variant 0.22
thyX 3067762 c.184C>A synonymous_variant 0.2
thyX 3067765 p.Leu61Ile missense_variant 0.18
thyX 3067774 p.Ala58Thr missense_variant 0.18
thyX 3067781 c.165C>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448441 c.-63A>G upstream_gene_variant 0.18
Rv3083 3449657 p.Ala385Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474517 p.Asp171Asn missense_variant 0.22
Rv3236c 3613273 c.-157C>A upstream_gene_variant 0.2
fbiB 3642703 c.1173_1174delCG frameshift_variant 0.15
alr 3840259 c.1160_1161dupAC frameshift_variant 0.2
clpC1 4040763 c.-59C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242977 c.-256C>T upstream_gene_variant 0.11
embB 4246818 p.Ala102Val missense_variant 0.12
embB 4246935 p.Thr141Met missense_variant 0.12
aftB 4267283 c.1554C>G synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408058 c.144delT frameshift_variant 0.29
gid 4408152 c.51C>T synonymous_variant 0.17