TB-Profiler result

Run: SRR19428497

Summary

Run ID: SRR19428497

Sample name:

Date: 03-04-2023 21:38:09

Number of reads: 359476

Percentage reads mapped: 99.46

Strain: lineage4.1.2.1

Drug-resistance: Other


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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 2288710 c.530_531delCC frameshift_variant 0.13 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 5391 p.Asp51Val missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8090 c.789C>G synonymous_variant 0.25
gyrA 9255 p.Asn652Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9332 c.2031C>T synonymous_variant 0.17
gyrA 9377 c.2076A>G synonymous_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759890 c.84A>G synonymous_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760294 p.Asn163Ser missense_variant 0.13
rpoB 760815 p.Glu337Gln missense_variant 0.13
rpoB 761635 p.Val610Ala missense_variant 0.15
rpoB 762810 p.Ala1002Ser missense_variant 0.33
rpoC 764200 c.831G>A synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765332 p.Gly655Ser missense_variant 0.17
rpoC 767183 p.Val1272Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776790 p.Val564Ala missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800811 c.3G>A start_lost 0.11
fbiC 1303825 p.Glu299* stop_gained 0.11
atpE 1461102 p.Gly20Ser missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474773 n.1116C>G non_coding_transcript_exon_variant 0.22
fabG1 1673439 c.-1G>C upstream_gene_variant 0.1
fabG1 1673760 p.Lys107Asn missense_variant 0.15
inhA 1673877 c.-325C>A upstream_gene_variant 0.18
rpsA 1833583 c.42C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102634 p.Gly137Ser missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170438 p.Gly59Cys missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289887 c.-649_-647delCCG upstream_gene_variant 0.1
pncA 2290032 c.-791A>G upstream_gene_variant 0.18
kasA 2518064 c.-51G>T upstream_gene_variant 0.1
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726195 c.3G>A start_lost 0.12
ahpC 2726651 c.459G>T synonymous_variant 0.13
folC 2747072 p.Gly176Asp missense_variant 0.13
folC 2747083 c.516G>T synonymous_variant 0.14
folC 2747472 p.Ile43Val missense_variant 0.2
Rv2752c 3064772 p.Ala474Pro missense_variant 0.12
Rv2752c 3066171 c.21G>A synonymous_variant 0.12
thyX 3068056 c.-111C>A upstream_gene_variant 0.2
thyA 3073766 p.Asp236Tyr missense_variant 0.13
thyA 3073955 p.Gly173Cys missense_variant 0.11
thyA 3074279 p.Gly65Cys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087032 c.213G>A synonymous_variant 0.14
ald 3087490 p.Glu224Gly missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475043 p.Gly346Asp missense_variant 0.17
whiB7 3568626 c.53delT frameshift_variant 0.12
Rv3236c 3612366 p.Leu251Val missense_variant 0.11
fbiA 3641383 p.Ala281Thr missense_variant 0.11
fbiB 3641427 c.-108C>T upstream_gene_variant 0.1
alr 3841483 c.-63C>T upstream_gene_variant 0.15
rpoA 3877971 c.537C>T synonymous_variant 0.13
clpC1 4040283 p.Leu141Pro missense_variant 0.12
embC 4241660 c.1798C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244282 c.1050C>A synonymous_variant 0.11
embA 4245178 p.Met649Lys missense_variant 0.18
embB 4247576 p.Leu355Val missense_variant 0.1
embB 4247998 c.1485C>G synonymous_variant 0.12
embB 4249432 c.2919A>C synonymous_variant 0.18
aftB 4267688 c.1149G>C synonymous_variant 0.13
ethA 4326188 p.Arg429Gln missense_variant 0.12
ethA 4327008 p.Asp156Tyr missense_variant 0.29
ethA 4328456 c.-983G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407907 p.Glu99Gly missense_variant 0.18