TB-Profiler result

Run: SRR6045052
Summary

Run ID: SRR6045052

Sample name:

Date: 04-04-2023 11:52:03

Number of reads: 2213864

Percentage reads mapped: 87.35

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.97
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.97
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
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.5 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.13
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.15
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.21
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.3
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.32
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.49
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.49
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.49
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.52
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.53
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.57
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.57
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.59
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.59
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.59
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.62
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.6
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.65
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.65
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.65
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.65
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.65
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.63
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.54
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.54
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.42
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.1
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.11
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.11
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.22
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.22
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.22
rrl 1474551 n.894G>A non_coding_transcript_exon_variant 0.18
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.33
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.43
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.29
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.29
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.25
rrl 1475187 n.1530C>T non_coding_transcript_exon_variant 0.12
rrl 1475188 n.1531C>G non_coding_transcript_exon_variant 0.12
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.18
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.18
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.18
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.21
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.23
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.25
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.18
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.18
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.18
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.17
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.17
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.36
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.33
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.38
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.44
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.45
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.46
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.51
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.51
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.46
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.46
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.46
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.46
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.43
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.39
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.39
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.46
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.47
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.47
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.56
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.57
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.6
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.64
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.61
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.55
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.1
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.1
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.1
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.1
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290079 c.-838T>C upstream_gene_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.96