TB-Profiler result

Run: SRR1163142
Summary

Run ID: SRR1163142

Sample name:

Date: 02-04-2023 23:32:28

Number of reads: 2169358

Percentage reads mapped: 98.88

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
gid 4407997 p.Gly69Asp missense_variant 1.0 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 0.97
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 0.98
rpoC 764840 p.Ile491Val missense_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 1472876 n.1031G>A non_coding_transcript_exon_variant 0.12
rrl 1473860 n.203C>A non_coding_transcript_exon_variant 0.14
rrl 1473870 n.213G>A non_coding_transcript_exon_variant 0.12
rrl 1473994 n.337C>T non_coding_transcript_exon_variant 0.13
rrl 1474663 n.1006C>A non_coding_transcript_exon_variant 0.15
rrl 1476239 n.2582T>C non_coding_transcript_exon_variant 0.13
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.15
rrl 1476483 n.2826G>T non_coding_transcript_exon_variant 0.15
rrl 1476668 n.3011C>A non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878581 c.-74C>G upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327472 c.2T>G start_lost 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0