TB-Profiler result

Run: ERR5987249
Summary

Run ID: ERR5987249

Sample name:

Date: 02-04-2023 01:28:34

Number of reads: 1117240

Percentage reads mapped: 67.56

Strain: lineage4.3.2

Drug-resistance: MDR-TB

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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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
rpoC 762899 c.-471G>C upstream_gene_variant 0.22
rpoC 762923 c.-447C>G upstream_gene_variant 0.23
rpoB 762925 p.Thr1040Ile missense_variant 0.23
rpoC 762929 c.-441G>C upstream_gene_variant 0.23
rpoB 762939 p.Met1045Leu missense_variant 0.22
rpoB 762942 p.Ile1046Val missense_variant 0.22
rpoC 762965 c.-405T>C upstream_gene_variant 0.22
rpoC 762980 c.-390T>C upstream_gene_variant 0.2
rpoC 762983 c.-387C>T upstream_gene_variant 0.22
rpoC 762989 c.-381G>C upstream_gene_variant 0.22
rpoC 762998 c.-372G>A upstream_gene_variant 0.19
rpoB 763005 p.Cys1067Val missense_variant 0.19
rpoC 763013 c.-357C>T upstream_gene_variant 0.18
rpoB 763014 p.Met1070Leu missense_variant 0.17
rpoB 763017 p.Gln1071Glu missense_variant 0.17
rpoC 763028 c.-342T>C upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.1
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.25
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.31
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.42
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.42
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.41
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.41
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.41
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.39
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.31
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.31
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.32
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.31
rrl 1476525 n.2868A>C non_coding_transcript_exon_variant 0.31
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.31
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.3
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.29
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.3
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.29
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.24
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.21
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.21
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0