TB-Profiler result

Run: SRR1196587
Summary

Run ID: SRR1196587

Sample name:

Date: 03-04-2023 05:29:32

Number of reads: 1167513

Percentage reads mapped: 96.45

Strain: lineage4.3.3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.96 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761547 p.Val581Met missense_variant 0.97
rpoB 762362 p.Glu852Asp missense_variant 0.13
rpoB 762369 c.2563T>C synonymous_variant 0.12
rpoC 762395 c.-975G>C upstream_gene_variant 0.17
rpoC 762398 c.-972T>C upstream_gene_variant 0.18
rpoC 762401 c.-969G>C upstream_gene_variant 0.16
rpoC 762404 c.-966T>C upstream_gene_variant 0.16
rpoC 762410 c.-960T>C upstream_gene_variant 0.15
rpoC 762416 c.-954A>G upstream_gene_variant 0.13
rpoC 762419 c.-951C>G upstream_gene_variant 0.12
rpoC 762434 c.-936T>C upstream_gene_variant 0.1
rpoC 764611 c.1242G>T synonymous_variant 0.15
rpoC 764650 c.1281G>C synonymous_variant 0.1
rpoC 764651 c.1282_1284delTCGinsAGC synonymous_variant 0.1
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
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.15
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.13
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3067313 c.633G>T synonymous_variant 0.11
thyX 3067316 c.630A>G synonymous_variant 0.11
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
rpoA 3877764 c.744C>G synonymous_variant 0.12
rpoA 3877770 c.738A>G synonymous_variant 0.13
rpoA 3877776 c.732T>C synonymous_variant 0.13
rpoA 3877782 c.726T>C synonymous_variant 0.14
rpoA 3877791 c.717C>G synonymous_variant 0.11
rpoA 3877818 c.690A>G synonymous_variant 0.11
rpoA 3877839 c.669G>C synonymous_variant 0.11
rpoA 3877857 c.651G>A synonymous_variant 0.1
rpoA 3878271 c.237T>C synonymous_variant 0.13
rpoA 3878284 p.Glu75Ala missense_variant 0.23
rpoA 3878292 c.216T>C synonymous_variant 0.21
rpoA 3878298 c.210A>G synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.15
rpoA 3878313 c.195G>C synonymous_variant 0.13
rpoA 3878322 c.186A>G synonymous_variant 0.12
rpoA 3878331 c.177A>G synonymous_variant 0.13
rpoA 3878334 c.174T>C synonymous_variant 0.13
rpoA 3878337 c.171T>C synonymous_variant 0.12
rpoA 3878346 c.162T>C synonymous_variant 0.17
rpoA 3878415 c.93C>T synonymous_variant 0.14
rpoA 3878424 c.84G>C synonymous_variant 0.14
rpoA 3878641 c.-134C>G upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242115 c.2253G>A 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
gid 4407912 c.160_290del frameshift_variant 1.0