TB-Profiler result

Run: SRR4035791

Summary

Run ID: SRR4035791

Sample name:

Date: 04-04-2023 07:18:06

Number of reads: 1318238

Percentage reads mapped: 99.44

Strain: lineage4.1.2

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 0.98
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.98
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 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576617 p.His424Asp missense_variant 0.2
mshA 576621 p.Ala425Val missense_variant 0.15
ccsA 620624 p.Ile245Thr missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762666 p.Pro954Ala missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767014 c.3645G>A synonymous_variant 0.15
rpoC 767021 p.Asp1218Tyr missense_variant 0.15
rpoC 767031 p.Leu1221Pro missense_variant 0.17
rpoC 767068 c.3699G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 779346 c.-866G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303024 c.97delG frameshift_variant 0.12
fbiC 1304460 c.1530C>G synonymous_variant 0.11
Rv1258c 1407053 c.288C>T synonymous_variant 0.17
Rv1258c 1407069 p.Leu91Gln missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154649 p.Lys488Arg missense_variant 0.12
katG 2155046 p.Lys356Gln missense_variant 0.17
katG 2155057 p.Gln352Leu missense_variant 0.14
PPE35 2168010 p.Ser868Asn missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290031 c.-790A>T upstream_gene_variant 0.19
kasA 2518076 c.-39C>T upstream_gene_variant 0.95
kasA 2519231 p.Tyr373His missense_variant 0.11
eis 2715574 c.-242T>C upstream_gene_variant 0.15
Rv2752c 3065236 p.Ser319Trp missense_variant 0.12
Rv2752c 3065994 p.His66Gln missense_variant 0.11
Rv2752c 3066029 p.Pro55Ser missense_variant 0.13
thyX 3067276 p.Pro224Thr missense_variant 0.18
thyX 3067320 p.Arg209Pro missense_variant 0.14
thyX 3067864 p.Asp28Tyr missense_variant 0.2
thyA 3074044 p.Leu143Pro missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339544 p.Arg143Trp missense_variant 0.15
fbiD 3339561 c.444C>T synonymous_variant 0.17
Rv3083 3449163 c.660G>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474553 c.547T>C synonymous_variant 0.14
fprA 3474740 p.Cys245Tyr missense_variant 0.2
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
clpC1 4039686 p.Arg340His missense_variant 0.15
clpC1 4039692 p.Leu338Pro missense_variant 0.15
clpC1 4040301 p.Arg135His missense_variant 0.18
embC 4240046 p.Pro62Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242831 p.Ala990Glu missense_variant 0.2
embA 4245786 p.Ala852Thr missense_variant 0.15
embB 4246682 p.Asp57Asn missense_variant 0.17
embB 4246809 p.Leu99Pro missense_variant 0.11
embB 4248803 p.Met764Val missense_variant 0.11
embB 4249227 p.Pro905Arg missense_variant 0.14
ubiA 4269772 p.Ile21Thr missense_variant 0.1
ethA 4327115 p.Ile120Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408330 c.-128G>A upstream_gene_variant 0.18