TB-Profiler result

Run: SRR6981927
Summary

Run ID: SRR6981927

Sample name:

Date: 04-04-2023 18:22:01

Number of reads: 368650

Percentage reads mapped: 99.65

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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5071 c.-168_-161delGGACGTCG upstream_gene_variant 0.11
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6401 p.Cys388Arg missense_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7383 p.Tyr28His missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8716 p.Pro472His missense_variant 0.12
gyrA 8962 p.Ile554Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490883 p.Ser34Ile missense_variant 0.12
fgd1 491755 p.Gln325Lys missense_variant 0.13
ccsA 619831 c.-60T>G upstream_gene_variant 0.3
rpoB 759611 c.-196G>C upstream_gene_variant 0.2
rpoB 760744 p.Lys313Arg missense_variant 0.12
rpoC 763711 c.342G>T synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776623 c.1858C>T synonymous_variant 0.15
mmpL5 776677 p.Ser602Pro missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303107 p.Cys59* stop_gained 0.14
fbiC 1303374 c.444T>C synonymous_variant 0.1
fbiC 1304992 p.Ser688Pro missense_variant 0.11
embR 1416826 c.522T>C synonymous_variant 0.13
embR 1416893 p.Asp152Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472207 n.362A>G non_coding_transcript_exon_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472487 n.642C>A non_coding_transcript_exon_variant 0.11
rrl 1473523 n.-134delC upstream_gene_variant 0.11
rrl 1474833 n.1176G>T non_coding_transcript_exon_variant 0.17
rrl 1475470 n.1813T>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102236 c.807C>A synonymous_variant 0.15
katG 2154781 p.Ala444Val missense_variant 0.11
katG 2155669 p.Leu148Pro missense_variant 0.11
katG 2156049 c.63C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289032 c.207_209delACC disruptive_inframe_deletion 0.12
eis 2714303 p.Asp344His missense_variant 0.12
ahpC 2726316 p.Glu42* stop_gained 0.12
folC 2747367 p.Val78Leu missense_variant 0.13
folC 2747650 c.-52G>A upstream_gene_variant 0.11
Rv2752c 3064844 p.Asp450Tyr missense_variant 0.12
thyX 3067679 p.Cys89* stop_gained 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087711 p.Val298Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612453 p.Val222Met missense_variant 0.2
fbiB 3642772 p.Asp413Ala missense_variant 0.33
alr 3840240 p.Pro394Gln missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040031 p.Val225Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243690 c.461dupG frameshift_variant 0.12
embA 4243835 c.603G>A synonymous_variant 0.12
embB 4249209 p.Val899Glu missense_variant 0.12
embB 4249344 p.Val944Ala missense_variant 0.13
embB 4249552 c.3039C>A synonymous_variant 0.14
aftB 4267070 c.1767C>A synonymous_variant 0.11
aftB 4267464 c.1371_1372delCA frameshift_variant 0.13
ubiA 4269433 p.Met134Thr missense_variant 0.17
ethA 4326839 p.Ile212Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407968 c.235T>C synonymous_variant 0.1
gid 4408156 p.Leu16Arg missense_variant 1.0
PPE35 2165166 c.859_*2482del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0