TB-Profiler result

Run: SRR4033219
Summary

Run ID: SRR4033219

Sample name:

Date: 04-04-2023 05:55:28

Number of reads: 888750

Percentage reads mapped: 99.77

Strain: lineage4.8.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
lineage4.8.1 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
gyrA 6937 c.-365G>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 761953 p.Ala716Val missense_variant 0.12
rpoC 766003 c.2634G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775823 c.2658G>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476476 n.2819G>T non_coding_transcript_exon_variant 0.12
tlyA 1917952 p.Ala5Ser missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156378 c.-267T>A upstream_gene_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168481 p.Val711Ala missense_variant 0.1
PPE35 2169320 p.Leu431Phe missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519240 p.Pro376Ser missense_variant 0.17
folC 2747011 c.587delC frameshift_variant 0.12
folC 2747283 p.Glu106* stop_gained 0.14
Rv2752c 3066322 c.-131G>A upstream_gene_variant 0.11
thyX 3067886 c.60A>C synonymous_variant 0.18
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fprA 3474561 c.555G>A synonymous_variant 0.15
fbiB 3642874 p.Leu447Arg missense_variant 1.0
alr 3841578 c.-158G>A upstream_gene_variant 0.11
embC 4241436 p.Ala525Asp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246257 p.Pro1009Ser missense_variant 0.12
ethA 4328178 c.-705G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0