TB-Profiler result

Run: SRR12199455
Summary

Run ID: SRR12199455

Sample name:

Date: 03-04-2023 06:41:38

Number of reads: 156523

Percentage reads mapped: 58.69

Strain:

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
lineage3.1.2 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.29 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
gyrB 6280 c.1041T>C synonymous_variant 0.67
gyrA 7496 c.195C>T synonymous_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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.23
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.2
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.21
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.21
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.29
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.41
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.38
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.29
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.29
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.29
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.27
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.29
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.27
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.27
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.27
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.32
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.32
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.38
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.2
rrl 1473679 n.22T>C non_coding_transcript_exon_variant 0.5
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.27
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.4
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.4
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.23
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.25
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.28
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.3
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154399 c.1713C>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156027 p.Pro29Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169302 p.Met437Ile missense_variant 0.33
PPE35 2169658 p.Val319Ile missense_variant 0.67
PPE35 2169662 c.951T>C synonymous_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 0.4
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.67
PPE35 2170247 p.Ile122Val missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473958 c.-49C>T upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.23
rpoA 3877731 c.777G>A synonymous_variant 0.4
clpC1 4038871 p.Glu612Lys missense_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244276 c.1044A>C synonymous_variant 0.67
embA 4244281 p.Gly350Val missense_variant 0.67
embB 4247383 p.Trp290* stop_gained 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408114 p.Gly30Asp missense_variant 1.0