TB-Profiler result

Run: SRR1181130
Summary

Run ID: SRR1181130

Sample name:

Date: 03-04-2023 04:30:56

Number of reads: 4227444

Percentage reads mapped: 92.41

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.23 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.11 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 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu 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 1472123 n.278A>T non_coding_transcript_exon_variant 0.1
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.19
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.23
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.18
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472971 n.1126G>A non_coding_transcript_exon_variant 0.12
rrs 1472972 n.1127T>C non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.17
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.13
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.19
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.25
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.26
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.11
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.15
rrl 1474286 n.629C>G non_coding_transcript_exon_variant 0.11
rrl 1474287 n.630T>C non_coding_transcript_exon_variant 0.11
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.18
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.14
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.13
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.13
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.1
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.1
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.13
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.18
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.13
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.11
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.1
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rrl 1476523 n.2867delC non_coding_transcript_exon_variant 0.11
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.11
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.11
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170102 p.Pro171Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G 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 3641973 c.443_445dupTCA disruptive_inframe_insertion 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244087 c.855G>A synonymous_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249678 c.3165C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0