TB-Profiler result

Run: SRR2101520
Summary

Run ID: SRR2101520

Sample name:

Date: 03-04-2023 23:45:57

Number of reads: 384709

Percentage reads mapped: 99.81

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491710 p.Phe310Leu missense_variant 0.12
fgd1 491755 p.Gln325* stop_gained 0.2
ccsA 620371 p.Ala161Thr missense_variant 0.1
ccsA 620748 c.858T>G synonymous_variant 0.3
rpoB 762761 p.Cys985Trp missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.11
mmpL5 777548 c.933G>A synonymous_variant 1.0
mmpL5 777595 p.Glu296Lys missense_variant 1.0
mmpS5 778610 p.Ala99Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303781 p.Phe284Ser missense_variant 0.15
Rv1258c 1406485 p.Pro286Ser missense_variant 0.12
atpE 1461087 p.Leu15Met missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473546 n.-112G>A upstream_gene_variant 0.22
rrl 1473973 n.316T>C non_coding_transcript_exon_variant 0.18
rrl 1475951 n.2294G>T non_coding_transcript_exon_variant 0.18
rrl 1476545 n.2888C>A non_coding_transcript_exon_variant 0.18
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.1
fabG1 1673746 p.Glu103Lys missense_variant 0.2
rpsA 1834435 c.894G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103111 c.-69G>A upstream_gene_variant 0.13
katG 2154246 c.1866T>C synonymous_variant 0.12
katG 2156002 p.Asp37Gly missense_variant 0.22
PPE35 2169553 p.Pro354Thr missense_variant 1.0
Rv1979c 2222222 c.882_942delCATCGGAAACGCTACCTTCCGAACGATCATCGTCGTCGGAGCCCTGATATCGATGTTCGGC frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289558 c.-318delT upstream_gene_variant 0.13
pncA 2289789 c.-548C>A upstream_gene_variant 0.15
ahpC 2726218 p.Gln9Leu missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.25
folC 2746229 p.Ala457Val missense_variant 0.18
folC 2747368 c.231G>A synonymous_variant 0.12
ribD 2986946 p.Asp36Glu missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086855 c.36C>T synonymous_variant 0.12
Rv3083 3448779 c.276C>T synonymous_variant 0.11
Rv3083 3449882 p.Trp460* stop_gained 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568654 p.Gln9Arg missense_variant 0.11
whiB7 3568735 c.-56G>A upstream_gene_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3613020 p.Ile33Phe missense_variant 0.12
Rv3236c 3613122 c.-6G>T upstream_gene_variant 0.12
fbiA 3641024 p.Asp161Gly missense_variant 0.13
fbiA 3641281 p.Ile247Val missense_variant 0.15
fbiA 3641382 p.Cys280Trp missense_variant 0.17
alr 3840719 c.702A>G synonymous_variant 1.0
ddn 3986835 c.-9A>G upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243374 p.Gly48Cys missense_variant 0.25
ethR 4327768 p.Thr74Ser missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0