TB-Profiler result

Run: SRR11349193
Summary

Run ID: SRR11349193

Sample name:

Date: 02-04-2023 20:55:01

Number of reads: 2064746

Percentage reads mapped: 57.66

Strain: lineage4.1.2

Drug-resistance: RR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.13 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.25 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 7323 p.Pro8Ala missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9155 c.1854C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776659 p.Asp608Asn 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 1472124 n.279C>T non_coding_transcript_exon_variant 0.11
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.1
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.16
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.18
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.17
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.17
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.19
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.2
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.17
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.21
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.3
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.21
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.14
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.1
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.19
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.2
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.21
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.17
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.15
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.16
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.18
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.21
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.23
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.19
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.2
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.26
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.25
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.23
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.26
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.23
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.14
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.15
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.15
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.15
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.12
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.18
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.17
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.19
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.16
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.22
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.2
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.14
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.18
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.18
rrl 1476165 n.2508T>C non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.26
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.26
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.25
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.18
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.17
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.17
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.21
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.14
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.15
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.18
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.14
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.22
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.15
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.3
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.23
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.35
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.35
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.28
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.16
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.14
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.14
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.1
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.11
rrl 1476600 n.2943A>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168501 p.Phe704Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642316 p.Arg261Lys missense_variant 1.0
rpoA 3878381 c.127C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243290 p.Ser20Ala missense_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4247121 p.Ser203Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0