TB-Profiler result

Run: SRR6896390

Summary

Run ID: SRR6896390

Sample name:

Date: 04-04-2023 18:04:33

Number of reads: 486050

Percentage reads mapped: 96.96

Strain: lineage4.3.2.1

Drug-resistance: Sensitive


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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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 0.98
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
gyrB 5520 p.Pro94Leu missense_variant 0.91
gyrB 6186 p.His316Arg missense_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7973 c.672A>G synonymous_variant 0.11
gyrA 7975 p.Gly225Asp missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491706 c.924G>T synonymous_variant 0.22
mshA 575653 c.306G>A synonymous_variant 0.18
mshA 576471 c.1125dupC frameshift_variant 0.17
rpoB 760609 p.Leu268Pro missense_variant 0.14
rpoB 761128 p.Ser441* stop_gained 0.11
rpoC 763807 c.438T>C synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767201 p.Ala1278Pro missense_variant 0.12
rpoC 767218 c.3849C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775986 p.His832Arg missense_variant 0.1
mmpL5 777371 c.1110C>A synonymous_variant 0.12
mmpL5 777597 p.Arg295Gln missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303943 p.Val338Glu missense_variant 0.13
Rv1258c 1406228 c.1113C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473766 n.109G>T non_coding_transcript_exon_variant 0.17
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 0.12
rrl 1475097 n.1440G>T non_coding_transcript_exon_variant 0.15
rrl 1475120 n.1463G>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102826 c.217C>A synonymous_variant 0.12
katG 2155224 p.Met296Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289408 c.-167C>A upstream_gene_variant 0.11
pncA 2289825 c.-584A>G upstream_gene_variant 0.14
pncA 2290107 c.-866T>A upstream_gene_variant 1.0
eis 2715050 p.Gly95Arg missense_variant 0.18
eis 2715324 c.9G>T synonymous_variant 0.11
folC 2746524 p.Ala359Thr missense_variant 0.14
pepQ 2860308 c.111C>T synonymous_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073930 p.Tyr181Phe missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448358 c.-146G>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568774 c.-95G>T upstream_gene_variant 0.15
Rv3236c 3612391 c.726G>T synonymous_variant 0.12
fbiB 3641301 c.-234C>A upstream_gene_variant 0.13
rpoA 3877736 p.Val258Leu missense_variant 0.1
ddn 3986693 c.-151C>A upstream_gene_variant 0.12
ddn 3986907 c.66_67delAC frameshift_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039279 p.Val476Ile missense_variant 0.1
panD 4044380 c.-99C>A upstream_gene_variant 0.12
embC 4239951 p.Arg30Gln missense_variant 0.12
embC 4240365 p.Phe168Tyr missense_variant 0.14
embC 4241343 c.1484delG frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243031 c.3173delG frameshift_variant 0.2
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.14
embC 4243092 p.Leu1077Arg missense_variant 0.11
embC 4243095 p.Gly1078Val missense_variant 0.11
embA 4243099 c.-134G>C upstream_gene_variant 0.12
embA 4243102 c.-131G>T upstream_gene_variant 0.12
embC 4243103 p.Thr1081Pro missense_variant 0.12
embC 4243106 p.Arg1082Ser missense_variant 0.12
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.13
embA 4243460 c.228C>T synonymous_variant 0.13
embB 4245782 c.-732C>A upstream_gene_variant 0.15
embB 4247000 p.Gly163Trp missense_variant 0.15
aftB 4267815 p.Ala341Val missense_variant 0.25
aftB 4268250 p.Ala196Val missense_variant 0.12
aftB 4268361 p.Ser159* stop_gained 0.17
aftB 4268904 c.-68C>A upstream_gene_variant 0.12
ubiA 4269092 p.Phe248Ile missense_variant 0.12
ubiA 4269959 c.-126C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408359 c.-157G>T upstream_gene_variant 0.17