TB-Profiler result

Run: SRR19303792
Summary

Run ID: SRR19303792

Sample name:

Date: 03-04-2023 21:06:47

Number of reads: 319813

Percentage reads mapped: 9.33

Strain: lineage4.1.2.1

Drug-resistance: Sensitive

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
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 8041 p.Gly247Ala missense_variant 0.33
gyrA 8468 p.His389Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490780 c.-3C>T upstream_gene_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762141 p.Asp779Tyr missense_variant 0.29
rpoC 763517 p.Lys50* stop_gained 0.22
rpoC 763840 c.471G>A synonymous_variant 0.22
rpoC 765150 p.Gly594Glu missense_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
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.33
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.67
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.67
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.6
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.6
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.5
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.33
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.25
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.22
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.22
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.2
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.22
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.25
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.25
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.62
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.5
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.5
rrl 1475894 n.2237C>A non_coding_transcript_exon_variant 0.43
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.5
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 1.0
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.92
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.92
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.92
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.89
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.89
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.88
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.89
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.89
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.89
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.88
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.93
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.88
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156107 p.Pro2Leu missense_variant 0.25
PPE35 2169079 p.Thr512Ala missense_variant 0.4
Rv1979c 2221853 p.Phe438Ile missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289128 c.114G>C synonymous_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726241 p.Ala17Thr missense_variant 0.18
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449747 p.Asp415Val missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474530 p.Arg175His missense_variant 0.25
rpoA 3877874 p.Gly212Arg missense_variant 0.22
rpoA 3878389 p.Arg40His missense_variant 0.2
clpC1 4038386 c.2319G>A synonymous_variant 0.22
clpC1 4039988 c.717C>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248395 p.Phe628Val missense_variant 0.33
ethA 4326534 p.Thr314Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407673 p.Val177Gly missense_variant 0.25