TB-Profiler result

Run: SRR19303779
Summary

Run ID: SRR19303779

Sample name:

Date: 03-04-2023 21:06:20

Number of reads: 993913

Percentage reads mapped: 38.96

Strain: lineage4.8

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
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 7147 c.-155G>C upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576456 p.Val370Gly missense_variant 0.18
mshA 576613 c.1266A>C synonymous_variant 0.33
rpoC 764367 p.Gly333Ala missense_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.18
rpoC 764536 c.1167G>C synonymous_variant 0.2
rpoC 764537 p.Pro390Val missense_variant 0.35
rpoC 764540 p.Val391Ile missense_variant 0.32
rpoC 764548 c.1179G>C synonymous_variant 0.3
rpoC 764549 p.Pro394Ala missense_variant 0.27
rpoC 764552 p.Gly395Asn missense_variant 0.29
rpoC 764557 p.Asn396Lys missense_variant 0.27
rpoC 764566 c.1197C>G synonymous_variant 0.27
rpoC 764575 c.1206T>C synonymous_variant 0.25
rpoC 764576 p.Ser403Ala missense_variant 0.25
rpoC 764581 c.1212T>C synonymous_variant 0.24
rpoC 764582 p.Leu405Met missense_variant 0.27
rpoC 764605 c.1236G>C synonymous_variant 0.28
rpoC 764611 c.1242G>C synonymous_variant 0.29
rpoC 764620 c.1251G>C synonymous_variant 0.24
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.24
rpoC 764632 c.1263T>C synonymous_variant 0.24
rpoC 764641 c.1272C>T synonymous_variant 0.24
rpoC 764650 c.1281G>T synonymous_variant 0.21
rpoC 764671 c.1302G>C synonymous_variant 0.17
rpoC 764672 p.Gln435Glu missense_variant 0.18
rpoC 764677 c.1308C>G synonymous_variant 0.18
rpoC 764686 c.1317C>T synonymous_variant 0.17
rpoC 764689 c.1320G>A synonymous_variant 0.18
rpoC 764695 c.1326T>C synonymous_variant 0.18
rpoC 764701 c.1332C>G synonymous_variant 0.18
rpoC 764705 p.Leu446Lys missense_variant 0.18
rpoC 764716 c.1347G>C synonymous_variant 0.16
rpoC 764719 c.1350G>A synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302885 c.-46G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.13
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.44
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.45
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.43
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.43
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.43
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.32
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
fabG1 1673553 p.Asp38Glu missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.24
Rv2752c 3064875 c.1317C>G synonymous_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 1.0
fbiA 3641477 p.Asp312Gly missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4246529 p.Ser6Gly missense_variant 0.5
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4248324 p.Ala604Gly missense_variant 0.25
embB 4248328 c.1815G>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0