TB-Profiler result

Run: SRR16295825
Summary

Run ID: SRR16295825

Sample name:

Date: 03-04-2023 17:18:22

Number of reads: 5938298

Percentage reads mapped: 75.5

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 0.99
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 0.16 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 8306 c.1005C>T synonymous_variant 0.11
gyrA 8533 p.Ser411Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575164 c.-183delC upstream_gene_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.51
mshA 576111 p.Ala255Gly missense_variant 0.23
ccsA 620243 p.Cys118Tyr missense_variant 0.12
rpoB 760337 c.531C>A synonymous_variant 0.12
rpoB 760924 p.Arg373His missense_variant 0.18
rpoB 762952 p.Gln1049Arg missense_variant 0.11
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 779336 c.349delC 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 1304065 p.Ala379Thr missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407500 c.-160C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.21
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.21
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.15
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.15
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.16
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.15
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.15
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.16
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.16
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.16
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrl 1475287 n.1630G>C non_coding_transcript_exon_variant 0.11
rrl 1475289 n.1632G>C non_coding_transcript_exon_variant 0.11
rrl 1475290 n.1633A>C non_coding_transcript_exon_variant 0.12
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.22
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.23
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.2
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.2
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.2
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.19
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.19
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.19
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.19
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.19
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.34
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.35
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.36
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.37
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.4
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.28
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.28
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.28
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.27
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.28
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.28
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.46
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.45
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.54
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.49
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.51
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.51
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.51
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.52
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.42
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.42
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.38
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.37
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.37
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.36
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.37
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.37
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.36
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.37
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.31
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.28
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.28
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.27
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.26
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.23
fabG1 1673681 p.Pro81Gln missense_variant 0.12
inhA 1674487 p.Gly96Arg missense_variant 0.14
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
PPE35 2170035 p.Val193Ala missense_variant 0.2
PPE35 2170054 p.Thr187Ser missense_variant 0.21
PPE35 2170292 c.321G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289025 p.Val73Ile missense_variant 0.12
pncA 2289064 p.Gly60Ser missense_variant 0.12
pncA 2290170 c.-929T>A upstream_gene_variant 0.12
kasA 2518348 c.234A>T synonymous_variant 0.24
kasA 2518424 p.Asp104Asn missense_variant 0.18
eis 2714780 p.Gln185* stop_gained 0.12
eis 2715467 c.-135A>G upstream_gene_variant 1.0
folC 2746845 p.Ala252Thr missense_variant 0.15
Rv2752c 3064631 p.Ala521Thr missense_variant 0.16
Rv2752c 3064636 p.Val519Ala missense_variant 0.2
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
rpoA 3878569 c.-62C>G upstream_gene_variant 0.45
rpoA 3878654 c.-147A>G upstream_gene_variant 0.13
embC 4241284 c.1422G>A synonymous_variant 0.14
embC 4241301 p.Ala480Val missense_variant 0.12
embC 4242564 p.Ala901Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4247024 p.Pro171Ala missense_variant 0.26
embB 4247033 p.Ser174Arg missense_variant 0.21
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269541 p.Pro98His missense_variant 0.13
ubiA 4269697 p.Tyr46Cys missense_variant 0.1
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethR 4327617 p.Asp23Glu missense_variant 0.11
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