TB-Profiler result

Run: SRR10033120

Summary

Run ID: SRR10033120

Sample name:

Date: 02-04-2023 14:23:15

Number of reads: 1436522

Percentage reads mapped: 86.82

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 5746 c.507A>G synonymous_variant 0.2
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778083 p.Pro133Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417528 c.-181C>T upstream_gene_variant 0.12
atpE 1461044 c.-1A>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474264 n.607T>C non_coding_transcript_exon_variant 0.33
rrl 1474446 n.789C>T non_coding_transcript_exon_variant 0.2
rrl 1475464 n.1807A>T non_coding_transcript_exon_variant 0.13
rrl 1475682 n.2025A>G non_coding_transcript_exon_variant 0.13
rrl 1476027 n.2370G>A non_coding_transcript_exon_variant 0.22
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.18
rpsA 1834908 p.Ser456Leu missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103037 p.Ser2Arg missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860131 c.288C>T synonymous_variant 0.14
Rv2752c 3064751 p.Arg481Cys missense_variant 1.0
thyA 3074410 p.Arg21Leu missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448603 p.Leu34Phe missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640379 c.-164T>C upstream_gene_variant 1.0
fbiA 3640810 p.Gln90Lys missense_variant 0.1
clpC1 4038589 p.Arg706Cys missense_variant 0.11
clpC1 4040384 c.321C>T synonymous_variant 0.12
embC 4239670 c.-193C>T upstream_gene_variant 0.12
embC 4242074 p.Arg738Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.18