TB-Profiler result

Run: ERR4815289
Summary

Run ID: ERR4815289

Sample name:

Date: 01-04-2023 13:46:44

Number of reads: 590931

Percentage reads mapped: 95.07

Strain: lineage3

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
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 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 7117 p.Met626Ile missense_variant 0.2
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 490620 c.-163T>G upstream_gene_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 0.9
rpoB 760426 p.Glu207Gly missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764293 c.924G>C synonymous_variant 0.33
rpoC 765167 p.Gln600* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776341 c.2139dupG frameshift_variant 0.15
mmpL5 777614 c.867C>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800670 c.-139C>T upstream_gene_variant 0.22
fbiC 1303831 c.903delC frameshift_variant 0.17
fbiC 1305279 c.2350dupA frameshift_variant 0.12
embR 1417247 p.Lys34Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.43
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.57
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.62
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.62
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.83
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.83
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.83
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.83
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.6
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.4
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.33
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.33
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.67
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.67
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 0.5
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.5
rrl 1475970 n.2313C>A non_coding_transcript_exon_variant 0.33
fabG1 1673560 p.Lys41Leu missense_variant 0.18
rpsA 1834273 c.732C>T synonymous_variant 1.0
rpsA 1834815 p.His425Pro missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.22
ndh 2103130 c.-88C>T upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155519 p.Trp198Leu missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170371 p.Thr81Val missense_variant 0.15
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
kasA 2518787 p.Arg225Trp missense_variant 0.33
kasA 2519269 c.1155C>T synonymous_variant 0.2
eis 2714278 p.Asp352Gly missense_variant 0.12
eis 2714307 c.1026G>T synonymous_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726181 c.-12A>G upstream_gene_variant 0.12
folC 2747249 p.Pro117Leu missense_variant 0.11
Rv2752c 3065300 p.Asp298Asn missense_variant 0.11
thyX 3067328 c.618G>A synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448992 c.489C>T synonymous_variant 0.22
Rv3083 3449563 p.Gly354Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475167 c.1161C>A synonymous_variant 0.17
whiB7 3568725 c.-46A>C upstream_gene_variant 0.33
fbiB 3641337 c.-198G>T upstream_gene_variant 0.22
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4038406 p.Val767Leu missense_variant 0.11
embC 4240483 c.621G>C synonymous_variant 0.17
embC 4240648 c.786C>T synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247165 p.Lys218* stop_gained 0.25
embB 4247450 p.Ala313Thr missense_variant 0.13
embB 4247706 p.Phe398Ser missense_variant 0.14
embB 4248880 c.2367G>T synonymous_variant 0.14
aftB 4267276 p.Leu521Met missense_variant 0.12
ubiA 4269622 p.Leu71Pro missense_variant 0.14
ethA 4326585 p.Pro297Thr missense_variant 0.11
ethA 4328239 c.-766G>T upstream_gene_variant 0.11
ethA 4328445 c.-972A>C upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0