TB-Profiler result

Run: ERR2229768
Summary

Run ID: ERR2229768

Sample name:

Date: 31-03-2023 17:34:42

Number of reads: 488220

Percentage reads mapped: 99.12

Strain: lineage4

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
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 8741 c.1440C>A synonymous_variant 0.22
mshA 575268 c.-80C>A upstream_gene_variant 0.22
rpoB 761875 p.Val690Gly missense_variant 0.29
rpoC 766777 c.3408C>G synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.2
mmpL5 775727 c.2754C>G synonymous_variant 0.2
mmpL5 775927 c.2554C>T synonymous_variant 0.13
mmpL5 777885 p.Ala199Ile missense_variant 0.18
mmpL5 777888 p.Gln198Leu missense_variant 0.18
mmpL5 777891 p.Gln197Leu missense_variant 0.17
mmpL5 777894 p.Gln196Leu missense_variant 0.18
mmpL5 777896 p.Asp195Gly missense_variant 0.18
mmpL5 778276 p.Ala69Ser missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406529 p.Gly271Ala missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476416 n.2759C>A non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.56
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103079 c.-37T>A upstream_gene_variant 0.2
katG 2154827 p.Pro429Thr missense_variant 0.2
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.33
PPE35 2167967 c.2646A>C synonymous_variant 0.36
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.3
PPE35 2169272 c.1341C>G synonymous_variant 0.3
PPE35 2169278 c.1335T>C synonymous_variant 0.45
PPE35 2169281 c.1332T>G synonymous_variant 0.45
PPE35 2169287 c.1326T>C synonymous_variant 0.17
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170147 p.Ser156Ala missense_variant 0.2
PPE35 2170505 p.Thr36Met missense_variant 0.12
PPE35 2170508 c.105A>C synonymous_variant 0.15
PPE35 2170528 p.Ser29Thr missense_variant 0.15
Rv1979c 2222375 p.Gly264Ser missense_variant 0.12
Rv1979c 2223261 c.-97A>G upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290060 c.-819C>A upstream_gene_variant 0.22
pncA 2290064 c.-823C>T upstream_gene_variant 0.22
pncA 2290069 c.-828C>T upstream_gene_variant 0.22
kasA 2518879 c.765A>G synonymous_variant 0.29
kasA 2518882 c.768C>A synonymous_variant 0.29
eis 2714485 p.Arg283Gln missense_variant 0.18
eis 2715432 c.-100C>T upstream_gene_variant 0.17
eis 2715436 c.-104G>A upstream_gene_variant 0.17
ahpC 2726670 p.Glu160* stop_gained 0.17
thyX 3067384 p.Asn188His missense_variant 0.67
thyX 3067952 c.-7G>T upstream_gene_variant 0.18
thyX 3067954 c.-9G>C upstream_gene_variant 0.2
thyX 3067955 c.-10G>C upstream_gene_variant 0.2
thyX 3067957 c.-12A>C upstream_gene_variant 0.2
fbiD 3339047 c.-70delC upstream_gene_variant 0.17
Rv3083 3448473 c.-31C>A upstream_gene_variant 0.33
fprA 3474469 p.Asn155Asp missense_variant 0.18
alr 3840348 c.1072delG frameshift_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.24
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3877715 p.Lys265Glu missense_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.17
clpC1 4039530 p.Asp392Ala missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.21
clpC1 4039654 p.Thr351Ser missense_variant 0.23
clpC1 4040797 c.-93T>C upstream_gene_variant 0.12
embC 4240847 p.Asp329His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246428 p.Ala1066Ser missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4249341 p.Ala943Asp missense_variant 0.25
aftB 4266975 p.Pro621Leu missense_variant 0.18
aftB 4267647 p.Asp397Val missense_variant 0.12
aftB 4267987 c.849delG frameshift_variant 1.0
ethA 4326339 p.Asn379Asp missense_variant 0.29
ethA 4326489 p.Ser329Pro missense_variant 0.18
ethR 4326961 c.-588G>C upstream_gene_variant 0.29
ethR 4326964 c.-585G>A upstream_gene_variant 0.29
ethR 4326970 c.-579G>T upstream_gene_variant 0.29
ethR 4327898 p.His117Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407600 c.603C>T synonymous_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0