TB-Profiler result

Run: SRR21675426

Summary

Run ID: SRR21675426

Sample name:

Date: 04-04-2023 02:34:36

Number of reads: 174549

Percentage reads mapped: 99.35

Strain: lineage4

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
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
ethA 4326522 c.951delT frameshift_variant 0.33 ethionamide
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 5150 c.-90G>T upstream_gene_variant 0.25
gyrB 5517 p.Ile93Thr missense_variant 0.29
gyrB 6621 p.Asp461Gly missense_variant 0.14
gyrB 6860 c.1623delC frameshift_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7840 p.Gly180Val missense_variant 0.17
mshA 575904 p.Ala186Val missense_variant 0.18
rpoB 759634 c.-173A>G upstream_gene_variant 0.5
rpoB 761040 p.Ile412Val missense_variant 0.25
rpoB 761883 p.Gly693Cys missense_variant 0.33
rpoB 762048 c.2243delA frameshift_variant 0.22
rpoC 763223 c.-147C>A upstream_gene_variant 0.15
rpoC 764454 p.Ala362Val missense_variant 0.29
rpoC 764822 p.Asp485Tyr missense_variant 0.4
rpoC 766736 c.3367C>A synonymous_variant 0.17
rpoC 766836 p.Val1156Gly missense_variant 0.5
rpoC 767080 c.3713_3730delTCAACTGCCGCAGCGATA disruptive_inframe_deletion 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775991 p.Glu830Asp missense_variant 0.25
mmpL5 776572 p.Met637Leu missense_variant 0.2
mmpR5 778406 c.-584G>T upstream_gene_variant 0.5
mmpR5 778995 p.Ser2Arg missense_variant 0.5
mmpL5 779064 c.-584G>T upstream_gene_variant 0.33
mmpR5 779201 p.Ala71Asp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406949 p.Ala131Val missense_variant 0.18
embR 1416222 p.Phe376Leu missense_variant 0.5
embR 1416232 p.Cys372Gly missense_variant 0.5
embR 1416259 c.1089G>C synonymous_variant 0.5
embR 1416262 c.1086G>C synonymous_variant 0.5
embR 1417417 c.-70C>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472884 n.1039G>A non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474882 n.1225A>T non_coding_transcript_exon_variant 0.13
rrl 1475412 n.1755G>T non_coding_transcript_exon_variant 0.2
rrl 1475893 n.2236A>G non_coding_transcript_exon_variant 0.33
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.11
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1674101 p.Val221Ala missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103023 p.Pro7Leu missense_variant 0.22
ndh 2103085 c.-44delA upstream_gene_variant 0.33
ndh 2103239 c.-197T>A upstream_gene_variant 0.15
PPE35 2167749 p.Asn955Ser missense_variant 0.2
PPE35 2168075 c.2538G>T synonymous_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2222038 p.Gly376Asp missense_variant 0.33
Rv1979c 2222050 p.Leu372Pro missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223328 c.-164C>T upstream_gene_variant 0.18
pncA 2289401 c.-160G>T upstream_gene_variant 0.22
pncA 2289918 c.-677A>G upstream_gene_variant 1.0
pncA 2290089 c.-848G>T upstream_gene_variant 0.33
kasA 2518399 p.Trp95Cys missense_variant 0.22
kasA 2518881 p.Ala256Asp missense_variant 0.22
eis 2714228 c.1105T>C synonymous_variant 1.0
eis 2714550 c.783C>A synonymous_variant 0.67
pepQ 2860381 p.Gln13Arg missense_variant 0.29
ribD 2986820 c.-19A>G upstream_gene_variant 0.22
ribD 2986898 c.60G>T synonymous_variant 0.18
Rv2752c 3064699 p.Ser498Tyr missense_variant 0.22
Rv2752c 3065353 p.Arg280Gln missense_variant 0.5
Rv2752c 3065484 c.708G>A synonymous_variant 0.25
Rv2752c 3065803 p.Glu130Gly missense_variant 0.33
ald 3086977 p.Ala53Val missense_variant 0.4
ald 3087823 p.Ser335* stop_gained 0.33
fbiD 3339131 p.Pro5Leu missense_variant 0.33
fbiD 3339454 p.Leu113Met missense_variant 0.22
fbiD 3339716 p.Gln200Leu missense_variant 1.0
whiB7 3568669 p.Leu4Arg missense_variant 0.14
whiB7 3568764 c.-85T>C upstream_gene_variant 0.33
Rv3236c 3613284 c.-169delC upstream_gene_variant 0.17
fbiB 3641642 c.108G>A synonymous_variant 0.17
fbiB 3641843 p.Gln103His missense_variant 0.5
fbiB 3642708 p.Gly392Trp missense_variant 0.14
alr 3840373 p.Leu350Met missense_variant 0.25
rpoA 3877805 p.Gly235Trp missense_variant 0.5
rpoA 3878207 p.Gly101Cys missense_variant 0.33
rpoA 3878363 p.Ala49Ser missense_variant 0.25
ddn 3986927 p.Met28Ile missense_variant 0.29
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240291 c.429G>T synonymous_variant 0.25
embC 4241704 c.1842C>A synonymous_variant 0.4
embC 4241889 p.Ala676Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242948 p.Gly1029Asp missense_variant 0.25
embA 4243693 p.Gly154Ala missense_variant 0.25
embA 4244505 p.Gly425Trp missense_variant 0.4
embA 4244598 p.Leu456Met missense_variant 0.29
embA 4244894 c.1662C>T synonymous_variant 0.5
embA 4244964 p.Ala578Ser missense_variant 0.5
embB 4245515 c.-999C>T upstream_gene_variant 0.15
embB 4247521 c.1008G>A synonymous_variant 0.25
aftB 4267194 p.Pro548Gln missense_variant 0.33
ubiA 4269316 p.Ser173Tyr missense_variant 0.5
ubiA 4269847 c.-14A>G upstream_gene_variant 0.5
ethA 4327986 c.-513G>A upstream_gene_variant 0.2
ethA 4328470 c.-997G>C upstream_gene_variant 0.18
whiB6 4338538 c.-17T>C upstream_gene_variant 0.5
whiB6 4338557 c.-36C>T upstream_gene_variant 0.5
gid 4407862 c.339_340dupGA frameshift_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0