TB-Profiler result

Run: ERR4815296
Summary

Run ID: ERR4815296

Sample name:

Date: 01-04-2023 13:47:02

Number of reads: 235811

Percentage reads mapped: 87.81

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 6703 c.-599G>C upstream_gene_variant 0.29
gyrA 6706 c.-596G>A upstream_gene_variant 0.29
gyrA 6709 c.-593A>G upstream_gene_variant 0.4
gyrA 6712 c.-590G>C upstream_gene_variant 0.4
gyrA 6727 c.-575G>T upstream_gene_variant 0.4
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.4
gyrA 6739 c.-563C>T upstream_gene_variant 0.4
gyrA 6745 c.-557T>C upstream_gene_variant 0.4
gyrA 6754 c.-548C>T upstream_gene_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7391 c.90C>T synonymous_variant 0.29
gyrA 7394 c.93T>C synonymous_variant 0.29
gyrA 7397 c.96G>C synonymous_variant 0.29
gyrA 7403 c.102C>T synonymous_variant 0.33
gyrA 7412 c.111C>G synonymous_variant 0.4
gyrA 7421 c.120G>C synonymous_variant 0.33
gyrA 7424 c.123G>C synonymous_variant 0.33
gyrA 7427 c.126G>C synonymous_variant 0.33
gyrA 7433 c.132G>C synonymous_variant 0.4
gyrA 7439 c.138C>T synonymous_variant 0.4
gyrA 7442 c.141G>C synonymous_variant 0.4
mshA 576584 c.1241delG frameshift_variant 0.4
ccsA 620396 p.Ser169Phe missense_variant 0.4
ccsA 620645 p.Glu252Val missense_variant 0.4
rpoB 760753 p.Leu316Arg missense_variant 0.4
rpoB 761612 c.1806G>T synonymous_variant 0.22
rpoB 761615 c.1809A>C synonymous_variant 0.29
rpoC 763094 c.-276G>C upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.22
rpoC 763127 c.-243G>C upstream_gene_variant 0.29
rpoC 763136 c.-234C>T upstream_gene_variant 0.29
rpoC 763145 c.-225G>A upstream_gene_variant 0.29
rpoC 763157 c.-213G>T upstream_gene_variant 0.29
rpoC 763166 c.-204A>G upstream_gene_variant 0.33
rpoC 763172 c.-198G>C upstream_gene_variant 0.4
rpoC 767284 c.3915C>G synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777374 p.Glu369Asp missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406099 c.1242C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 1.0
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 1.0
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 1.0
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 1.0
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
fabG1 1673761 p.Val108Phe missense_variant 0.33
rpsA 1833625 c.84A>G synonymous_variant 0.5
rpsA 1833709 c.168C>T synonymous_variant 0.29
rpsA 1833919 c.378C>T synonymous_variant 0.2
ndh 2102635 c.408C>G synonymous_variant 0.33
ndh 2102638 c.405A>T synonymous_variant 0.33
ndh 2102641 p.Phe134Trp missense_variant 0.33
ndh 2102662 c.381C>A synonymous_variant 0.5
ndh 2102668 c.375T>C synonymous_variant 0.33
ndh 2102671 c.372T>C synonymous_variant 0.33
ndh 2102680 c.363T>G synonymous_variant 0.33
ndh 2102683 c.360T>A synonymous_variant 0.33
ndh 2102686 c.357G>C synonymous_variant 0.33
ndh 2102689 c.354C>G synonymous_variant 0.33
ndh 2102692 c.351C>G synonymous_variant 0.4
ndh 2102707 c.336C>T synonymous_variant 0.25
ndh 2103084 c.-43_-42insCGTAGTAGCTAAC upstream_gene_variant 1.0
katG 2154072 c.2040C>T synonymous_variant 0.4
PPE35 2168149 p.Pro822Ser missense_variant 1.0
kasA 2518871 p.His253Asn missense_variant 0.4
thyX 3067827 p.Gly40Asp missense_variant 0.5
Rv3083 3448322 c.-182G>A upstream_gene_variant 1.0
fprA 3473894 c.-113G>C upstream_gene_variant 0.25
Rv3236c 3612136 c.981C>T synonymous_variant 0.15
Rv3236c 3612972 c.145T>C synonymous_variant 0.33
fbiA 3640787 p.Arg82His missense_variant 0.17
fbiB 3642413 c.879G>A synonymous_variant 0.33
rpoA 3878259 c.249G>C synonymous_variant 0.5
rpoA 3878271 c.237T>C synonymous_variant 0.5
rpoA 3878283 p.Glu75Asp missense_variant 0.5
rpoA 3878292 c.216T>C synonymous_variant 0.5
rpoA 3878298 c.210A>G synonymous_variant 0.43
rpoA 3878301 c.207C>G synonymous_variant 0.43
rpoA 3878310 c.198G>T synonymous_variant 0.33
rpoA 3878313 c.195G>C synonymous_variant 0.33
rpoA 3878322 c.186A>G synonymous_variant 0.4
clpC1 4038737 c.1968C>T synonymous_variant 0.5
clpC1 4038740 c.1965G>C synonymous_variant 0.67
clpC1 4038749 c.1956C>A synonymous_variant 0.4
clpC1 4038755 c.1950G>C synonymous_variant 0.4
clpC1 4038767 c.1938G>C synonymous_variant 0.4
clpC1 4038770 c.1935C>T synonymous_variant 0.4
clpC1 4038773 c.1932T>C synonymous_variant 0.4
clpC1 4038782 c.1923G>T synonymous_variant 0.4
clpC1 4038790 c.1915C>T synonymous_variant 0.29
clpC1 4038795 p.Ser637Thr missense_variant 0.25
embA 4245056 c.1824C>A synonymous_variant 0.29
embA 4245063 c.1831C>T synonymous_variant 0.29
aftB 4267496 c.1341A>G synonymous_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0