TB-Profiler result

Run: SRR3675590
Summary

Run ID: SRR3675590

Sample name:

Date: 04-04-2023 05:35:27

Number of reads: 910005

Percentage reads mapped: 95.89

Strain: lineage4.8.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 6922 c.-380G>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779144 p.Ser52Tyr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801195 c.387G>A synonymous_variant 1.0
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.12
Rv1258c 1406946 p.Ala132Gly missense_variant 0.12
embR 1417346 c.1delA frameshift_variant&start_lost 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.95
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.96
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.12
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.11
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.11
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.19
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.11
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.11
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.12
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.12
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.15
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.15
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.15
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.11
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.11
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.12
rpsA 1834879 c.1338C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.21
ribD 2987318 c.480C>T synonymous_variant 0.18
fbiD 3339040 c.-78T>C upstream_gene_variant 0.97
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3642874 p.Leu447Arg missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247066 p.Ile185Val missense_variant 0.11
ubiA 4269803 p.Ala11Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0