TB-Profiler result

Run: ERR4815577
Summary

Run ID: ERR4815577

Sample name:

Date: 01-04-2023 13:56:31

Number of reads: 1433194

Percentage reads mapped: 97.82

Strain: lineage3.1.3

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.3 East-African-Indian CAS RD750 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 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.13 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576750 p.Lys468Thr missense_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.16
Rv1258c 1406946 p.Ala132Gly missense_variant 0.16
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.17
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.17
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.13
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.12
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.18
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.18
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.17
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.18
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.17
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472719 n.874G>T non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.25
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.27
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.18
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.13
rrs 1473284 n.1439A>T non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.12
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.12
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.19
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.19
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.5
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.5
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.5
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.5
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.5
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.5
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.43
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.25
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.3
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.29
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.6
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.4
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.4
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.38
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.25
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.29
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.2
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.27
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.27
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.2
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.38
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.29
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.29
rrl 1475954 n.2297A>G non_coding_transcript_exon_variant 0.29
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.29
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.16
rpsA 1834159 c.618G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918474 p.Pro179Ser missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222732 c.432delT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
rpoA 3878567 c.-60C>G upstream_gene_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249195 c.2682C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407656 p.Ala183Ser missense_variant 1.0
gid 4408175 p.Ala10Pro missense_variant 1.0