TB-Profiler result

Run: SRR1169017
Summary

Run ID: SRR1169017

Sample name:

Date: 03-04-2023 02:38:14

Number of reads: 1588225

Percentage reads mapped: 58.42

Strain: lineage2.2.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 1472122 n.277G>C non_coding_transcript_exon_variant 0.11 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.45 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
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776517 p.Met655Thr missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.53
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.56
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.57
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.58
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.54
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.54
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.56
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.32
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.37
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.47
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.47
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.45
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.45
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.16
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.15
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.14
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.15
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.16
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.1
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.1
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.11
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.28
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.28
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.28
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.2
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.54
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.57
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.69
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.7
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.76
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.81
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.82
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.75
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.65
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.57
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.49
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.45
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.45
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.44
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.42
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.42
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.42
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.41
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.41
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.31
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.21
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.19
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.19
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102161 c.882G>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0