TB-Profiler result

Run: SRR2100093
Summary

Run ID: SRR2100093

Sample name:

Date: 03-04-2023 22:45:20

Number of reads: 4790090

Percentage reads mapped: 99.38

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
gyrB 5347 c.108G>C synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575932 p.Glu195Asp missense_variant 0.28
rpoB 759620 c.-187A>C upstream_gene_variant 0.36
rpoC 762836 c.-534C>G upstream_gene_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.38
Rv1979c 2222483 p.Ala228Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.23
eis 2714433 c.899delA frameshift_variant 1.0
eis 2715586 c.-254G>C upstream_gene_variant 0.28
ahpC 2726210 c.18T>C synonymous_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.15
Rv2752c 3064741 p.Gly484Ala missense_variant 0.36
thyX 3067995 c.-50A>C upstream_gene_variant 0.27
thyA 3073806 c.666C>G synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.26
fprA 3475280 p.Val425Gly missense_variant 0.36
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.3
fbiB 3642734 c.1200G>C synonymous_variant 0.21
fbiB 3642772 p.Asp413Ala missense_variant 0.27
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878238 p.Asp90Glu missense_variant 0.23
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.18
rpoA 3878601 c.-95delG upstream_gene_variant 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.41
embC 4239842 c.-21C>A upstream_gene_variant 0.24
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4242476 p.Pro872Ala missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embC 4242827 p.Leu989Val missense_variant 0.21
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0