TB-Profiler result

Run: SRR16295781
Summary

Run ID: SRR16295781

Sample name:

Date: 03-04-2023 17:04:48

Number of reads: 7401338

Percentage reads mapped: 91.64

Strain: lineage2.2.1

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
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 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 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 576108 p.Ala254Gly missense_variant 0.59
mshA 576111 p.Ala255Gly missense_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779196 c.209dupA frameshift_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.13
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.25
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.25
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.22
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.22
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.22
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.22
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.23
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.22
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.21
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.21
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.19
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.21
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.21
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.22
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.22
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.1
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 0.14
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 1476514 n.2857C>T non_coding_transcript_exon_variant 0.19
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.2
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.2
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.16
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.15
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.15
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.15
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.17
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.15
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.15
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.15
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
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
eis 2715467 c.-135A>G upstream_gene_variant 1.0
Rv2752c 3064636 p.Val519Ala missense_variant 0.11
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
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
alr 3840745 p.Gly226Trp missense_variant 0.11
rpoA 3878569 c.-62C>G upstream_gene_variant 0.3
rpoA 3878641 c.-134C>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.24
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246552 p.Asn13Lys missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.26
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4249751 c.3238T>C synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethA 4327050 p.Asn142Asp missense_variant 0.1
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