TB-Profiler result

Run: SRR16295792
Summary

Run ID: SRR16295792

Sample name:

Date: 03-04-2023 17:04:46

Number of reads: 4647863

Percentage reads mapped: 69.99

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 0.34 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
gyrB 5405 p.Glu56* stop_gained 0.25
gyrB 5937 p.Ala233Val missense_variant 0.12
gyrB 7218 p.Arg660His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8184 p.Lys295Glu missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491295 c.513C>A synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.63
mshA 576111 p.Ala255Gly missense_variant 0.29
rpoB 759609 c.-198C>A upstream_gene_variant 0.13
rpoB 759614 c.-193C>A upstream_gene_variant 0.14
rpoB 760689 p.Phe295Leu missense_variant 0.14
rpoB 761152 p.Leu449Gln missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763167 p.Glu1121* stop_gained 0.19
rpoB 763264 p.Ala1153Val missense_variant 0.15
rpoC 764292 p.Ser308* stop_gained 0.13
rpoC 764583 c.1215delG frameshift_variant 0.12
rpoC 764828 p.Leu487Phe missense_variant 0.14
rpoC 765843 p.Thr825Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777918 p.Gly188Asp missense_variant 0.15
mmpR5 779181 c.198delG frameshift_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781565 c.6A>T synonymous_variant 0.12
fbiC 1304477 p.Ala516Val missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407518 c.-178C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472101 n.256G>C non_coding_transcript_exon_variant 0.12
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.18
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.18
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.33
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.32
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.32
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.3
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.32
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.32
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.34
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.34
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.34
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.37
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.37
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.1
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrl 1474018 n.361G>A non_coding_transcript_exon_variant 0.11
rrl 1476072 n.2415T>A non_coding_transcript_exon_variant 0.21
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.23
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.29
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.26
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.23
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.23
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.23
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.23
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.23
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.23
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.24
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.23
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.23
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.24
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.24
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.44
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.45
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.47
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.47
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.46
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.47
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.48
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.37
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.35
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.35
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.36
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.35
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.31
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.31
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.32
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.32
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.32
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.54
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.55
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.58
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.54
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.63
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.64
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.58
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.59
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.59
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.59
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.59
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.56
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.57
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.57
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.57
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.59
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.51
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.48
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.45
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.44
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.4
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.39
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.27
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.22
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.19
inhA 1674779 p.Pro193His missense_variant 0.12
inhA 1674885 c.684C>A synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834274 p.Ile245Leu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103038 p.Ser2Ile missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168036 c.2577C>T synonymous_variant 0.14
PPE35 2170390 p.Trp75Gly missense_variant 0.14
PPE35 2170415 c.198A>G synonymous_variant 0.14
Rv1979c 2222296 p.Lys290Arg missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289574 c.-333T>C upstream_gene_variant 0.14
kasA 2518180 c.66G>A synonymous_variant 0.14
eis 2714936 p.Pro133Ser missense_variant 0.14
eis 2715467 c.-135A>G upstream_gene_variant 1.0
folC 2746190 p.Gly470Asp missense_variant 0.12
folC 2747320 c.279C>A synonymous_variant 0.17
pepQ 2860144 p.Val92Gly missense_variant 0.18
ribD 2986709 c.-130C>T upstream_gene_variant 0.12
ribD 2986848 p.Ser4Thr missense_variant 0.12
ribD 2987447 c.609C>T synonymous_variant 0.14
ribD 2987530 p.Pro231His missense_variant 0.14
ribD 2987567 c.729C>A synonymous_variant 0.18
thyX 3067965 c.-20C>T upstream_gene_variant 0.11
thyA 3074211 c.261A>T synonymous_variant 0.22
thyA 3074420 p.Lys18Gln missense_variant 0.14
thyA 3074464 p.Pro3Leu missense_variant 0.14
ald 3086762 c.-58C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339338 p.Gly74Val missense_variant 0.2
Rv3083 3449477 p.Thr325Asn missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474717 p.Asp237Glu missense_variant 0.12
fprA 3474792 c.786G>A synonymous_variant 0.12
Rv3236c 3612272 p.Val282Ala missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiB 3641457 c.-78G>A upstream_gene_variant 0.13
rpoA 3878569 c.-62C>G upstream_gene_variant 0.21
rpoA 3878641 c.-134C>G upstream_gene_variant 0.17
rpoA 3878648 c.-141C>G upstream_gene_variant 0.13
embC 4241452 c.1590G>A synonymous_variant 0.11
embC 4241933 p.Ala691Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243545 p.Leu105Met missense_variant 0.11
embA 4244144 c.912C>T synonymous_variant 0.12
embA 4244702 c.1470C>T synonymous_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4247028 p.Leu172Arg missense_variant 0.32
embB 4248043 c.1534delA frameshift_variant 0.12
embB 4248958 p.Trp815Cys missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268506 p.Arg111Trp missense_variant 0.2
ubiA 4269155 p.Thr227Pro missense_variant 0.23
ethA 4326438 p.Leu346Met missense_variant 0.12
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethR 4328149 p.Asp201Asn missense_variant 0.15
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