TB-Profiler result

Run: ERR4814878
Summary

Run ID: ERR4814878

Sample name:

Date: 01-04-2023 13:32:34

Number of reads: 1125518

Percentage reads mapped: 90.88

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
gyrA 7413 p.Gly38Ser missense_variant 0.11
gyrA 9155 c.1854C>G synonymous_variant 1.0
gyrA 9270 p.Asp657Asn missense_variant 0.13
mshA 575446 c.99A>T synonymous_variant 0.11
mshA 576444 p.Gly366Asp missense_variant 0.14
mshA 576725 p.Ile460Val missense_variant 1.0
ccsA 620228 p.Phe113Ser missense_variant 0.2
ccsA 620540 p.Arg217Leu missense_variant 0.14
rpoC 763622 p.Ala85Ser missense_variant 0.15
rpoC 763625 p.Lys86Glu missense_variant 0.1
rpoC 763642 c.273G>T synonymous_variant 0.31
rpoC 763648 c.279C>T synonymous_variant 0.38
rpoC 763654 c.285C>T synonymous_variant 0.45
rpoC 763657 p.Glu96Asp missense_variant 0.45
rpoC 763666 c.297G>C synonymous_variant 0.45
rpoC 763699 c.330G>T synonymous_variant 0.32
rpoC 763708 c.339G>A synonymous_variant 0.31
rpoC 763714 c.345G>C synonymous_variant 0.29
rpoC 763717 c.348T>C synonymous_variant 0.29
rpoC 763718 p.Leu117Val missense_variant 0.28
rpoC 763726 c.357C>T synonymous_variant 0.27
rpoC 763732 c.363C>T synonymous_variant 0.26
rpoC 763747 c.378G>A synonymous_variant 0.26
rpoC 763751 p.Ile128Val missense_variant 0.25
rpoC 763772 p.Val135Met missense_variant 0.17
rpoC 764485 c.1116G>C synonymous_variant 0.1
rpoC 764491 c.1122G>T synonymous_variant 0.11
rpoC 764500 c.1131C>T synonymous_variant 0.11
rpoC 764503 c.1134G>T synonymous_variant 0.12
rpoC 767291 p.Asp1308His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778086 c.394delG frameshift_variant 0.11
mmpL5 778348 p.Val45Ile missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302944 c.15delA frameshift_variant 0.22
fbiC 1303149 c.219C>T synonymous_variant 0.13
Rv1258c 1406887 p.Leu152Met missense_variant 0.14
Rv1258c 1407484 c.-144C>T upstream_gene_variant 0.11
embR 1416913 p.Trp145* stop_gained 0.12
embR 1417498 c.-151G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471971 n.126A>G non_coding_transcript_exon_variant 0.18
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.6
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.6
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.6
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.6
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.6
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.43
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.43
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.33
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.5
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.57
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.25
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.25
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.13
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrl 1473637 n.-21A>G upstream_gene_variant 0.14
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.67
rrl 1475757 n.2100_2101insGG non_coding_transcript_exon_variant 0.67
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 1.0
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.4
rpsA 1833570 p.Gln10Arg missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918460 p.Asp174Val missense_variant 0.11
ndh 2102315 p.Ile243Thr missense_variant 0.13
ndh 2102458 c.585C>T synonymous_variant 0.11
ndh 2102563 c.480G>T synonymous_variant 0.11
katG 2154185 p.Leu643Met missense_variant 0.12
katG 2154834 c.1278C>T synonymous_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223106 p.Val20Ala missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726259 p.Leu23Val missense_variant 0.11
folC 2747134 c.465C>A synonymous_variant 0.11
folC 2747586 p.Asn5Tyr missense_variant 0.18
Rv2752c 3065948 p.Gly82Trp missense_variant 0.13
ald 3087647 c.828A>G synonymous_variant 0.11
Rv3083 3448484 c.-20T>A upstream_gene_variant 1.0
fprA 3474398 p.Trp131* stop_gained 0.11
fprA 3475157 p.Lys384Met missense_variant 0.12
fprA 3475203 c.1197G>A synonymous_variant 0.12
fprA 3475376 c.1370G>A splice_region_variant&stop_retained_variant 0.13
Rv3236c 3612167 p.Gly317Val missense_variant 0.2
Rv3236c 3612290 p.Leu276Pro missense_variant 0.13
Rv3236c 3612708 c.409T>C synonymous_variant 0.1
fbiA 3641087 p.Thr182Met missense_variant 0.11
fbiB 3642107 c.573G>A synonymous_variant 0.11
fbiB 3642371 c.837G>T synonymous_variant 0.12
fbiB 3642759 p.Arg409Cys missense_variant 0.12
rpoA 3878201 p.Gly103Cys missense_variant 0.11
ddn 3986782 c.-62G>T upstream_gene_variant 0.11
clpC1 4039918 p.Gly263Cys missense_variant 0.11
embC 4241056 c.1194C>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243526 c.294G>T synonymous_variant 0.14
embA 4245454 p.Ala741Val missense_variant 0.11
aftB 4268557 p.Gly94* stop_gained 0.15
aftB 4268776 p.Ser21Gly missense_variant 0.12
ubiA 4269864 c.-31C>T upstream_gene_variant 1.0
ethR 4327576 p.Ser10Pro missense_variant 0.11
ethR 4328032 p.Ala162Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0