TB-Profiler result

Run: SRR19303784
Summary

Run ID: SRR19303784

Sample name:

Date: 03-04-2023 21:06:38

Number of reads: 2708340

Percentage reads mapped: 94.17

Strain: lineage4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.12 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
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 1.0
gyrA 7623 p.Pro108Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406247 p.Leu365Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.13
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.1
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.15
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.13
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.14
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.14
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.14
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.14
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.15
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.14
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.16
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.21
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.11
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.38
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.36
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.36
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.38
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.38
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.37
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.38
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.39
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.32
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.25
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.16
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.15
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.13
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.14
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.14
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.14
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.13
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.13
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.14
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.13
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.17
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.21
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.19
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.19
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.19
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.11
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.11
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.1
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155371 c.741C>T synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.69
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612113 c.1003dupG frameshift_variant 1.0
rpoA 3878680 c.-173C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0