TB-Profiler result

Run: SRR3675562
Summary

Run ID: SRR3675562

Sample name:

Date: 04-04-2023 05:33:35

Number of reads: 384600

Percentage reads mapped: 92.81

Strain: lineage4.3.1

Drug-resistance: Other

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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
lineage4.3.1 Euro-American (LAM) LAM9 None 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 streptomycin
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 5832 p.Ala198Val missense_variant 0.12
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 491250 c.468G>A synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775996 p.Ile829Val missense_variant 1.0
mmpR5 779404 p.Met139Leu missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302775 c.-156C>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.24
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.24
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.17
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.26
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.11
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.15
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.13
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.43
tlyA 1917814 c.-126C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103192 c.-150G>T upstream_gene_variant 0.25
katG 2155034 p.Gly360Cys missense_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747174 p.Ala142Gly missense_variant 0.86
Rv2752c 3066108 c.84C>T synonymous_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474565 p.Arg187Ser missense_variant 0.25
rpoA 3877829 p.Val227Ile missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0