TB-Profiler result

Run: SRR12199457
Summary

Run ID: SRR12199457

Sample name:

Date: 03-04-2023 06:41:39

Number of reads: 118031

Percentage reads mapped: 97.82

Strain: lineage4.9;lineage1.1

Drug-resistance: Sensitive

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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
lineage1 Indo-Oceanic EAI RD239 0.13
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.06
lineage4.9 Euro-American (H37Rv-like) T1 None 0.92
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
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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 777146 c.1335C>T synonymous_variant 1.0
mmpL5 777251 c.1230C>T synonymous_variant 1.0
embR 1416300 p.Val350Leu missense_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.5
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.5
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.5
rrs 1472447 n.602C>T non_coding_transcript_exon_variant 0.33
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.33
rrs 1472450 n.605A>G non_coding_transcript_exon_variant 0.33
rrs 1472451 n.606C>G non_coding_transcript_exon_variant 0.33
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.29
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.29
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.29
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.29
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.33
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.22
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.22
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.25
rrs 1472559 n.714T>G non_coding_transcript_exon_variant 0.25
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.4
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.29
rrs 1472935 n.1090G>T non_coding_transcript_exon_variant 0.25
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.25
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5
rrs 1473281 n.1436C>G non_coding_transcript_exon_variant 0.5
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.5
rrl 1473555 n.-103G>A upstream_gene_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.22
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.2
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.2
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.2
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.18
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.18
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.22
rrl 1476545 n.2888C>T non_coding_transcript_exon_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 1.0
PPE35 2170053 p.Thr187Ser missense_variant 1.0
Rv1979c 2222012 p.Gln385* stop_gained 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
pncA 2289987 c.-746C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714248 p.Gly362Glu missense_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.5
ahpC 2726350 p.Trp53Leu missense_variant 0.5
folC 2746745 p.Val285Gly missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087605 c.786G>A synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.33
ddn 3987101 c.258G>A synonymous_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247239 c.726G>A synonymous_variant 1.0
embB 4248359 p.Pro616Thr missense_variant 1.0
ubiA 4269288 p.Phe182Leu missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326421 c.1053G>T synonymous_variant 0.5
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0