TB-Profiler result

Run: ERR4815984
Summary

Run ID: ERR4815984

Sample name:

Date: 01-04-2023 14:10:35

Number of reads: 590352

Percentage reads mapped: 97.39

Strain: lineage4.3.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 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 0.64 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7428 c.128delA frameshift_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491008 c.231delC frameshift_variant 0.29
mshA 575332 c.-16T>C upstream_gene_variant 0.14
ccsA 620766 c.876C>A synonymous_variant 0.15
rpoB 762123 p.Glu773Lys missense_variant 0.15
rpoC 763794 p.Glu142Gly missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 c.2508G>A synonymous_variant 0.22
mmpL5 776023 p.Val820Leu missense_variant 0.17
mmpR5 778007 c.-983G>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801378 c.570C>T synonymous_variant 0.13
fbiC 1303723 p.Glu265* stop_gained 0.13
Rv1258c 1406534 c.807C>A synonymous_variant 0.2
Rv1258c 1407443 c.-103C>T upstream_gene_variant 0.17
embR 1416495 p.Gly285Cys missense_variant 0.12
atpE 1460931 c.-114A>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.92
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rpsA 1834390 c.849G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102778 p.Val89Phe missense_variant 0.11
katG 2155687 p.Asp142Gly missense_variant 0.2
PPE35 2169415 p.Gly400Cys missense_variant 0.15
Rv1979c 2222798 p.Pro123Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518979 p.Arg289Trp missense_variant 0.14
ahpC 2726084 c.-109C>A upstream_gene_variant 0.12
folC 2747068 p.Met177Ile missense_variant 0.12
folC 2747325 p.Arg92Ser missense_variant 0.12
ribD 2987033 c.195C>T synonymous_variant 0.2
ribD 2987296 p.Arg153His missense_variant 0.15
Rv2752c 3065753 p.Asn147Tyr missense_variant 0.14
Rv2752c 3066164 p.Pro10Ser missense_variant 0.11
Rv2752c 3066998 c.-807G>A upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087803 c.984C>A synonymous_variant 0.12
ald 3087865 p.Ala349Val missense_variant 0.11
fbiD 3339017 c.-101C>A upstream_gene_variant 0.11
Rv3083 3448484 c.-20T>G upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474545 p.Asp180Val missense_variant 0.13
fbiB 3641175 c.-360G>T upstream_gene_variant 0.29
fbiB 3641639 c.105G>A synonymous_variant 0.13
fbiB 3642577 p.Val348Ala missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038588 p.Arg706Phe missense_variant 0.17
embC 4240279 p.Leu139Phe missense_variant 0.22
embC 4240841 p.Tyr327His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embA 4245280 p.Arg683His missense_variant 0.18
embA 4246348 p.Thr1039Ile missense_variant 0.14
embB 4249386 p.Glu958Ala missense_variant 1.0
embB 4249412 p.Arg967Trp missense_variant 0.15
aftB 4267214 c.1623A>G synonymous_variant 0.1
aftB 4267249 p.Lys530Glu missense_variant 0.12
aftB 4268133 p.Leu235Pro missense_variant 0.12
ubiA 4269239 p.Ala199Thr missense_variant 0.25
ubiA 4269259 p.Arg192Leu missense_variant 0.25
ethA 4326678 p.Ser266Gly missense_variant 0.12
ethR 4326679 c.-870C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0