TB-Profiler result

Run: SRR13861241
Summary

Run ID: SRR13861241

Sample name:

Date: 03-04-2023 09:27:06

Number of reads: 1499799

Percentage reads mapped: 75.06

Strain: lineage4.9

Drug-resistance: HR-TB

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid
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 7466 c.165G>A synonymous_variant 0.12
gyrA 7469 c.168C>T synonymous_variant 0.12
gyrA 7472 c.171T>C synonymous_variant 0.13
gyrA 7475 c.174A>C synonymous_variant 0.13
gyrA 7480 p.Phe60Tyr missense_variant 0.14
gyrA 7484 c.183T>C synonymous_variant 0.15
gyrA 7487 c.186C>G synonymous_variant 0.14
gyrA 7490 c.189C>T synonymous_variant 0.13
gyrA 7523 c.222C>G synonymous_variant 0.13
gyrA 7949 c.648G>T synonymous_variant 0.92
gyrA 8123 p.Leu274Phe missense_variant 0.89
gyrA 8198 c.897T>C synonymous_variant 0.14
gyrA 9768 p.Gly823Cys missense_variant 1.0
rpoC 763594 c.225C>T synonymous_variant 0.11
rpoC 763633 c.264T>C synonymous_variant 0.12
rpoC 763636 c.267T>C synonymous_variant 0.12
rpoC 763642 c.273G>C synonymous_variant 0.13
rpoC 763658 c.289_291delCTTinsTTG synonymous_variant 0.18
rpoC 763675 c.306C>G synonymous_variant 0.15
rpoC 763696 c.327T>C synonymous_variant 0.17
rpoC 763702 c.333C>G synonymous_variant 0.16
rpoC 763708 c.339G>A synonymous_variant 0.14
rpoC 763709 c.340C>T synonymous_variant 0.14
rpoC 763714 c.345G>C synonymous_variant 0.17
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763723 c.354G>C synonymous_variant 0.15
rpoC 763732 c.363C>G synonymous_variant 0.17
rpoC 763734 p.Pro122Leu missense_variant 0.83
rpoC 763744 c.375G>C synonymous_variant 0.15
rpoC 765970 c.2601C>T synonymous_variant 0.12
rpoC 765994 c.2625A>T synonymous_variant 0.12
rpoC 766672 c.3303T>C synonymous_variant 0.13
rpoC 766726 c.3357T>C synonymous_variant 0.15
rpoC 766738 c.3369G>T synonymous_variant 0.15
rpoC 766750 c.3381C>G synonymous_variant 0.13
rpoC 766765 c.3396A>C synonymous_variant 0.13
rpoC 766801 c.3432C>A synonymous_variant 0.12
rpoC 766861 c.3492G>C synonymous_variant 0.13
rpoC 766963 c.3594T>C synonymous_variant 0.13
rpsL 781892 c.333A>G synonymous_variant 0.13
rpsL 781898 c.339A>T synonymous_variant 0.13
rpsL 781916 c.357T>C synonymous_variant 0.14
fbiC 1303914 c.984C>G synonymous_variant 0.13
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.13
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.16
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.15
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.14
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.16
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
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 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.35
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.34
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.34
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.34
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.34
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.34
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.34
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.34
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.33
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.34
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.34
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.37
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.35
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.36
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.48
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 1476369 n.2712C>T non_coding_transcript_exon_variant 0.58
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.57
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.45
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.53
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.54
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.26
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.25
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.24
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.25
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.26
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.26
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.26
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.22
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.22
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.22
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 0.98
rpsA 1834195 c.654G>C synonymous_variant 0.12
tlyA 1918034 p.Val32Ala missense_variant 1.0
katG 2155918 p.Ala65Val missense_variant 1.0
PPE35 2168767 p.Ser616Gly missense_variant 1.0
Rv1979c 2222377 p.Val263Gly missense_variant 1.0
ribD 2986993 p.Gly52Val missense_variant 1.0
Rv2752c 3065787 c.405G>C synonymous_variant 1.0
Rv2752c 3065993 p.Val67Ile missense_variant 0.13
Rv2752c 3065994 c.198T>C synonymous_variant 0.14
Rv3083 3448649 p.Arg49Pro missense_variant 1.0
Rv3236c 3613067 p.Val17Gly missense_variant 1.0
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0
fbiB 3642614 c.1080C>T synonymous_variant 0.14
fbiB 3642620 c.1086T>C synonymous_variant 0.14
clpC1 4038790 c.1915C>T synonymous_variant 0.12
clpC1 4039842 c.862_863insT frameshift_variant 0.98
panD 4044103 p.Ile60Ser missense_variant 0.98
embC 4240900 c.1038A>G synonymous_variant 0.13
embC 4241035 c.1173G>A synonymous_variant 0.12
embC 4241137 c.1275G>C synonymous_variant 0.13
embC 4241158 c.1296T>C synonymous_variant 0.13
embC 4241161 c.1299C>G synonymous_variant 0.13
embA 4245031 p.Arg600Gln missense_variant 0.98
gid 4408218 c.-16G>T upstream_gene_variant 1.0