TB-Profiler result

Run: SRR10315476
Summary

Run ID: SRR10315476

Sample name:

Date: 02-04-2023 17:06:36

Number of reads: 6792138

Percentage reads mapped: 89.25

Strain: lineage4.8

Drug-resistance: MDR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.18 streptomycin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6815 p.Lys526Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.2
rpoC 764840 p.Ile491Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.42
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.42
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.33
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.31
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.23
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472592 n.747C>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.38
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.38
rrs 1472604 n.759A>G non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.48
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.3
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.15
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.14
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.13
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.13
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.14
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.12
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.12
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.16
rrs 1472697 n.852T>C 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 0.21
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.14
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.13
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.15
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.15
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.15
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.11
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.11
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.11
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.11
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.15
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.11
rrl 1475003 n.1346G>T non_coding_transcript_exon_variant 0.12
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.16
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.15
rrl 1475716 n.2059A>T non_coding_transcript_exon_variant 0.15
rrl 1475749 n.2094_2108delCCCGTTAACCCGCAA non_coding_transcript_exon_variant 0.15
rrl 1475776 n.2119G>T non_coding_transcript_exon_variant 0.12
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.12
rrl 1475782 n.2125T>C non_coding_transcript_exon_variant 0.12
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.12
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.12
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1475963 n.2306G>C non_coding_transcript_exon_variant 0.14
rrl 1475973 n.2316T>A non_coding_transcript_exon_variant 0.13
rrl 1476127 n.2470C>T non_coding_transcript_exon_variant 0.15
rrl 1476237 n.2580C>A non_coding_transcript_exon_variant 0.11
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.16
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.16
rrl 1476279 n.2622G>T non_coding_transcript_exon_variant 0.14
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.27
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.13
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.22
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.22
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.23
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.23
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.26
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.23
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.24
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.21
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.25
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.3
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.49
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.29
rrl 1476404 n.2747G>A non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.28
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.2
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.2
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.19
rrl 1476474 n.2817C>T non_coding_transcript_exon_variant 0.2
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154769 p.Asp448Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3449368 p.Asn289Asp missense_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0