TB-Profiler result

Run: SRR4033888
Summary

Run ID: SRR4033888

Sample name:

Date: 04-04-2023 06:24:59

Number of reads: 1143392

Percentage reads mapped: 97.28

Strain: lineage4.3.2.1

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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 6481 c.-821G>A upstream_gene_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_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
gyrA 9505 c.2207_2208dupCG frameshift_variant 0.1
gyrA 9584 c.2285delT frameshift_variant 0.12
mshA 575315 c.-33G>A upstream_gene_variant 0.19
rpoB 762637 c.2836delG frameshift_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779127 c.-647A>G upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801229 p.Ala141Ser missense_variant 0.15
atpE 1461238 p.Phe65Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.17
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.21
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.21
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.19
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.19
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.19
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
inhA 1674416 p.Ala72Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918629 c.690G>T synonymous_variant 0.25
ndh 2103033 p.Gln4Lys missense_variant 0.14
katG 2155097 p.Tyr339His missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714572 p.Arg254Leu missense_variant 0.12
ahpC 2726293 p.Tyr34Cys missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087808 p.Arg330Leu missense_variant 0.11
fbiD 3339496 p.Glu127* stop_gained 0.12
Rv3083 3449072 c.571_572dupAC frameshift_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840269 c.1152C>T synonymous_variant 0.15
alr 3841311 p.Glu37Gly missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040010 p.Ala232Asp missense_variant 0.12
embC 4242425 p.Arg855Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244550 p.Ala440Ser missense_variant 0.12
embB 4246890 p.Thr126Asn missense_variant 0.11
embB 4247031 p.Arg173His missense_variant 0.29
aftB 4267553 c.1284C>T synonymous_variant 0.12
ubiA 4269967 c.-134C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0