TB-Profiler result

Run: SRR22424727
Summary

Run ID: SRR22424727

Sample name:

Date: 04-04-2023 04:09:11

Number of reads: 1226930

Percentage reads mapped: 91.33

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 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
rpoB 761140 p.His445Leu missense_variant 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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
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 576488 p.Val381Leu missense_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762143 c.2337T>C synonymous_variant 0.11
rpoB 762170 c.2364C>G synonymous_variant 0.11
rpoB 762176 c.2370T>G synonymous_variant 0.11
rpoB 762209 c.2403C>G synonymous_variant 0.12
rpoB 762224 c.2418C>G synonymous_variant 0.11
rpoB 762257 c.2451C>G synonymous_variant 0.11
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.29
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.33
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.18
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.15
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.24
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.22
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.22
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.18
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.16
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.43
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.43
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.43
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.43
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.5
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.33
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.33
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.33
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.33
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.33
rrl 1474664 n.1007G>T non_coding_transcript_exon_variant 0.33
rrl 1474666 n.1009T>G non_coding_transcript_exon_variant 0.33
rrl 1474670 n.1013C>G non_coding_transcript_exon_variant 0.33
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.29
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.29
rrl 1474679 n.1022G>C non_coding_transcript_exon_variant 0.25
rrl 1474684 n.1027T>C non_coding_transcript_exon_variant 0.29
rrl 1474687 n.1030C>A non_coding_transcript_exon_variant 0.29
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.38
rrl 1474711 n.1054G>T non_coding_transcript_exon_variant 0.38
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.22
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.29
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.4
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.4
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986827 c.-12G>A 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
rpoA 3878334 c.174T>C synonymous_variant 0.15
rpoA 3878391 c.117T>G synonymous_variant 0.11
rpoA 3878400 c.108T>C synonymous_variant 0.11
rpoA 3878406 c.102G>C synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407563 p.Gly214Arg missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407998 p.Gly69Ser missense_variant 1.0