TB-Profiler result

Run: ERR216953
Summary

Run ID: ERR216953

Sample name:

Date: 31-03-2023 15:56:46

Number of reads: 1003105

Percentage reads mapped: 47.78

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
gyrB 6140 p.Val301Leu missense_variant 1.0
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 490663 c.-120C>T upstream_gene_variant 0.18
fgd1 490872 c.90C>T synonymous_variant 0.12
mshA 575594 p.Gly83Ser missense_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778524 p.Ala128Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.57
Rv1258c 1406501 c.840G>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.15
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.15
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.17
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.3
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.31
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.32
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.31
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.26
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.35
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.39
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.43
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.43
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.44
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.59
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.59
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.74
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.74
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.61
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.65
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.65
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.56
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37
rrl 1476513 n.2856G>A non_coding_transcript_exon_variant 0.22
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.16
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.12
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.12
rrl 1476565 n.2908G>A non_coding_transcript_exon_variant 0.26
rrl 1476566 n.2909A>G non_coding_transcript_exon_variant 0.25
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.24
rrl 1476577 n.2920T>A non_coding_transcript_exon_variant 0.27
rrl 1476578 n.2921C>A non_coding_transcript_exon_variant 0.27
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.26
rrl 1476592 n.2935G>A non_coding_transcript_exon_variant 0.22
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.22
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.2
rrl 1476605 n.2948C>T non_coding_transcript_exon_variant 0.19
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.18
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.17
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.16
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.15
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.15
rrl 1476637 n.2980C>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917981 c.42G>T synonymous_variant 0.17
katG 2153933 p.Ala727Ser missense_variant 0.17
PPE35 2170283 c.330G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519364 c.1250G>T stop_lost&splice_region_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.37
folC 2746607 p.Ala331Asp missense_variant 0.17
folC 2746831 c.768G>A synonymous_variant 0.15
Rv2752c 3066147 c.45G>T synonymous_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.32
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087183 p.Thr122Ala missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474292 p.Arg96Cys missense_variant 0.12
whiB7 3568517 p.Ala55Ser missense_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641986 p.Thr151Ile missense_variant 0.2
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044422 c.-141C>T upstream_gene_variant 0.12
embC 4239842 c.-21C>A upstream_gene_variant 0.29
embC 4241138 p.Ala426Thr missense_variant 0.12
embC 4241653 c.1791C>T synonymous_variant 0.22
embC 4242142 p.Asp760Glu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243036 c.-197C>T upstream_gene_variant 0.15
embA 4243595 c.363G>A synonymous_variant 0.2
embA 4243938 p.Trp236Gly missense_variant 0.29
embB 4246569 p.Ala19Val missense_variant 0.25
embB 4247251 c.738C>T synonymous_variant 0.15
embB 4247627 p.Arg372Ser missense_variant 0.17
ubiA 4269902 c.-69G>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407786 c.417G>A synonymous_variant 0.2
gid 4408156 p.Leu16Arg missense_variant 1.0