TB-Profiler result

Run: SRR1062941
Summary

Run ID: SRR1062941

Sample name:

Date: 02-04-2023 18:41:49

Number of reads: 577220

Percentage reads mapped: 47.69

Strain: lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 0.94
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.97
lineage4.6.1.2 Euro-American T2 RD724 0.94
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
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid
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 6501 p.Arg421His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8754 p.Glu485Lys missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 0.92
gyrA 9351 p.Ser684Thr missense_variant 0.25
gyrA 9359 c.2058C>G synonymous_variant 0.25
mshA 575745 p.Ala133Asp missense_variant 0.14
rpoC 762887 c.-483G>C upstream_gene_variant 0.33
rpoC 762899 c.-471G>C upstream_gene_variant 0.43
rpoC 762917 c.-453C>G upstream_gene_variant 0.43
rpoC 762920 c.-450C>T upstream_gene_variant 0.38
rpoC 762923 c.-447C>G upstream_gene_variant 0.38
rpoB 762925 p.Thr1040Ile missense_variant 0.38
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.38
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776634 p.Asp616Gly missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304456 c.1528_1529delAC frameshift_variant 0.25
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.5
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.57
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.57
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.57
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.33
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.4
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.5
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.5
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.6
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.6
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.62
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.62
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.6
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.33
rrl 1475115 n.1458A>T non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.44
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.44
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.55
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.64
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.58
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.46
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.36
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.36
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154874 p.Tyr413Cys missense_variant 1.0
PPE35 2169545 p.His356Gln missense_variant 0.22
Rv1979c 2222757 c.408G>A synonymous_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289843 c.-602T>A upstream_gene_variant 0.5
kasA 2518755 p.Arg214Leu missense_variant 0.22
eis 2714881 p.Ala151Gly missense_variant 0.18
folC 2746590 p.Gly337Cys missense_variant 0.2
Rv2752c 3064672 p.Ala507Asp missense_variant 0.5
thyA 3073733 p.Val247Ile missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642565 p.Ala344Glu missense_variant 0.25
alr 3841014 p.Arg136Leu missense_variant 0.15
clpC1 4039619 c.1086G>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243547 c.315G>T synonymous_variant 0.14
embA 4245055 p.Thr608Asn missense_variant 1.0
embA 4246417 p.Arg1062Leu missense_variant 0.5
embB 4247491 c.978G>T synonymous_variant 0.22
ubiA 4269831 c.3G>T start_lost 0.18
ethA 4327155 p.Ala107Thr missense_variant 0.2
ethR 4328183 p.Tyr212Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0