TB-Profiler result

Run: ERR9117723
Summary

Run ID: ERR9117723

Sample name:

Date: 02-04-2023 09:29:32

Number of reads: 825891

Percentage reads mapped: 74.27

Strain: lineage4.1.1.3.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 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 0.12 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.15
fgd1 491027 p.Asn82Thr missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778079 c.-911C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801267 c.459A>G synonymous_variant 0.19
fbiC 1303601 p.Glu224Gly missense_variant 1.0
Rv1258c 1407084 p.Val86Ala missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.18
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.17
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.17
rrl 1474400 n.743T>A non_coding_transcript_exon_variant 0.12
rrl 1475709 n.2052T>G non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.33
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.33
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.42
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.42
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.42
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.42
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.36
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.27
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.25
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.21
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.21
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.18
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.12
fabG1 1674076 p.Thr213Pro missense_variant 0.33
inhA 1674415 p.Ala72Thr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170280 c.333C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289898 c.-657C>T upstream_gene_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.17
eis 2714221 p.Ala371Val missense_variant 0.13
eis 2714943 c.390C>A synonymous_variant 0.15
pepQ 2859722 c.696delT frameshift_variant 0.11
ribD 2986715 c.-124T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339688 p.Thr191Pro missense_variant 0.38
Rv3083 3448999 p.Pro166Thr missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474000 c.-7C>G upstream_gene_variant 0.1
fprA 3475275 p.Trp423* stop_gained 0.22
embC 4240633 p.Met257Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242774 p.Leu971Pro missense_variant 0.11
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267882 p.Gly319Arg missense_variant 0.15
aftB 4267993 p.Thr282Ser missense_variant 0.14
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0