TB-Profiler result

Run: SRR6045859
Summary

Run ID: SRR6045859

Sample name:

Date: 04-04-2023 12:06:50

Number of reads: 2979446

Percentage reads mapped: 96.53

Strain: lineage3

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
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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
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
embR 1416561 p.Lys263Glu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472543 n.699_700delCA non_coding_transcript_exon_variant 0.18
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.21
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.16
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.16
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.11
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.12
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.11
rrs 1472891 n.1046A>G non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrl 1474292 n.635T>C non_coding_transcript_exon_variant 0.4
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.33
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.33
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.4
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.33
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.5
rrl 1474634 n.977T>C non_coding_transcript_exon_variant 0.4
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.5
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.33
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.5
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.33
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.75
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.75
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.75
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.75
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.75
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.6
rrl 1475686 n.2029C>G non_coding_transcript_exon_variant 0.18
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.22
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.22
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.22
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.18
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.2
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.2
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.19
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.19
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.2
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.19
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.19
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474460 p.Val152Ile missense_variant 1.0
fbiA 3641453 p.Arg304Gln missense_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.29
embC 4241465 p.Phe535Ile missense_variant 1.0
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 4407588 c.615A>G synonymous_variant 1.0