TB-Profiler result

Run: SRR5451699
Summary

Run ID: SRR5451699

Sample name:

Date: 04-04-2023 10:25:00

Number of reads: 460907

Percentage reads mapped: 82.22

Strain: lineage4.5

Drug-resistance: Other

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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
lineage4.5 Euro-American H;T RD122 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
pncA 2289040 p.Trp68Arg missense_variant 0.12 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
gyrB 6824 p.Leu529Met missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 7939 p.Glu213Gly missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491066 p.Cys95Phe missense_variant 0.11
fgd1 491480 p.Ile233Asn missense_variant 0.17
fgd1 491595 c.813C>T synonymous_variant 0.15
ccsA 619786 c.-105G>C upstream_gene_variant 0.14
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 760118 c.312T>A synonymous_variant 0.17
rpoB 761749 p.Ser648Leu missense_variant 0.14
rpoB 762702 p.Val966Met missense_variant 1.0
rpoC 765509 p.Asp714Tyr missense_variant 0.12
rpoC 766774 c.3405T>A synonymous_variant 0.12
rpoC 767287 c.3918G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779344 p.Asp119Tyr missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
Rv1258c 1407395 c.-64_-56delTGCGGCAGC upstream_gene_variant 0.93
embR 1416406 c.942T>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472182 n.337A>T non_coding_transcript_exon_variant 0.12
rrl 1475604 n.1947A>T non_coding_transcript_exon_variant 0.11
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.17
rrl 1476070 n.2413A>T non_coding_transcript_exon_variant 0.22
rrl 1476380 n.2723G>T non_coding_transcript_exon_variant 0.22
inhA 1674193 c.-9A>T upstream_gene_variant 0.2
inhA 1674316 p.Thr39Ser missense_variant 0.11
rpsA 1833460 c.-82G>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101930 c.1113C>G synonymous_variant 0.17
katG 2154788 p.Val442Ile missense_variant 0.11
katG 2156379 c.-268A>G upstream_gene_variant 0.15
PPE35 2169718 p.Asn299Tyr missense_variant 0.25
PPE35 2170359 p.Gln85Leu missense_variant 0.11
PPE35 2170462 p.Gly51Trp missense_variant 0.14
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289003 p.Asp80Gly missense_variant 0.11
pncA 2289043 p.Ser67Thr missense_variant 0.12
folC 2746700 p.His300Arg missense_variant 0.11
folC 2747648 c.-50G>C upstream_gene_variant 0.11
ribD 2986647 c.-192G>A upstream_gene_variant 0.11
thyA 3074085 c.387C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475314 c.1308G>A synonymous_variant 0.12
Rv3236c 3613180 c.-64A>G upstream_gene_variant 0.11
fbiA 3640525 c.-18G>T upstream_gene_variant 0.18
rpoA 3877930 p.Ile193Thr missense_variant 0.11
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
ddn 3986966 c.123C>T synonymous_variant 0.2
ddn 3986997 p.Thr52Ser missense_variant 0.2
ddn 3987033 p.Leu64Ile missense_variant 0.17
clpC1 4038293 c.2412G>C synonymous_variant 0.25
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4038865 p.Val614Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244156 c.924A>T synonymous_variant 0.11
embA 4245772 p.Asn847Ile missense_variant 1.0
embA 4246312 p.Gly1027Asp missense_variant 0.17
embB 4246949 p.Gln146Glu missense_variant 0.14
aftB 4268621 p.Trp72Cys missense_variant 0.22
ethR 4328011 p.Ala155Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0