TB-Profiler result

Run: ERR4815408

Summary

Run ID: ERR4815408

Sample name:

Date: 01-04-2023 13:50:47

Number of reads: 499095

Percentage reads mapped: 96.25

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490724 c.-59G>A upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620500 p.Gly204Ser missense_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761542 p.Gln579Arg missense_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765450 p.Ala694Val missense_variant 0.25
rpoC 766502 p.Pro1045Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800807 c.-2C>A upstream_gene_variant 0.18
fbiC 1304074 p.Ala382Thr missense_variant 0.13
fbiC 1304784 c.1854T>C synonymous_variant 0.2
Rv1258c 1406333 p.Ile336Met missense_variant 0.2
embR 1416831 p.Ala173Thr missense_variant 0.15
embR 1417198 c.150A>G synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.5
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 1.0
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 1.0
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 1.0
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 1.0
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 1.0
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rpsA 1833918 p.Val126Ala missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918171 p.Ala78Thr missense_variant 0.13
tlyA 1918281 c.342A>G synonymous_variant 0.18
tlyA 1918606 p.Val223Phe missense_variant 0.11
ndh 2102372 p.Met224Thr missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167851 p.Asn921Ser missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168807 c.1805delT frameshift_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290212 c.-971G>A upstream_gene_variant 0.29
kasA 2518935 p.Ala274Asp missense_variant 0.14
kasA 2519158 c.1044C>T synonymous_variant 0.14
eis 2714316 c.1017G>A synonymous_variant 0.18
eis 2715472 c.-140A>G upstream_gene_variant 0.13
ahpC 2726017 c.-176C>A upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986720 c.-119C>G upstream_gene_variant 0.15
Rv2752c 3065099 c.1092delC frameshift_variant 0.5
thyX 3067572 p.Asp125Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087125 c.306T>C synonymous_variant 0.12
ald 3087348 p.Gly177Ser missense_variant 0.17
ald 3087648 p.Gly277Ser missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474210 p.Glu68Asp missense_variant 0.18
fprA 3475227 c.1221C>A synonymous_variant 0.12
Rv3236c 3612280 c.837C>A synonymous_variant 0.15
alr 3840371 c.1049delT frameshift_variant 0.29
ddn 3986693 c.-151C>T upstream_gene_variant 0.22
clpC1 4038327 p.Glu793Val missense_variant 0.13
clpC1 4040717 c.-13C>T upstream_gene_variant 0.29
embC 4239896 p.Val12Ile missense_variant 0.1
embC 4240374 p.Leu171Pro missense_variant 0.15
embC 4241390 c.1528C>T synonymous_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243944 p.Thr238Ala missense_variant 0.15
embA 4244749 p.Thr506Ile missense_variant 0.18
embB 4246650 p.Leu46Pro missense_variant 0.17
embB 4249293 p.Lys927Arg missense_variant 0.14
aftB 4267089 p.Thr583Ile missense_variant 0.18
aftB 4267776 p.Pro354Arg missense_variant 0.12
aftB 4268065 p.Ser258Thr missense_variant 0.17
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338486 c.36C>T synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408221 c.-19C>T upstream_gene_variant 0.22