TB-Profiler result

Run: SRR16962462
Summary

Run ID: SRR16962462

Sample name:

Date: 03-04-2023 17:48:16

Number of reads: 913562

Percentage reads mapped: 99.73

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 5472 p.Ala78Val missense_variant 1.0
gyrB 6348 p.Gln370Arg missense_variant 0.13
gyrB 6500 p.Arg421Cys missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491768 p.Ala329Val missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460892 c.-153A>G upstream_gene_variant 0.17
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472728 n.883G>C non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474909 n.1252C>T non_coding_transcript_exon_variant 0.2
rrl 1476264 n.2607A>G non_coding_transcript_exon_variant 0.2
rrl 1476569 n.2912G>T non_coding_transcript_exon_variant 0.17
inhA 1674425 p.Ala75Val missense_variant 0.17
rpsA 1833838 c.297G>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064708 p.Arg495Leu missense_variant 0.13
Rv2752c 3065775 p.Phe139Leu missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.5
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878252 p.Ser86Thr missense_variant 0.14
rpoA 3878260 p.Leu83Pro missense_variant 0.11
rpoA 3878641 c.-134C>G upstream_gene_variant 0.21
clpC1 4040282 c.423G>A synonymous_variant 1.0
embC 4241411 p.Ile517Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4248319 c.1806A>T synonymous_variant 0.36
embB 4248324 p.Ala604Gly missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0