TB-Profiler result

Run: SRR1175132
Summary

Run ID: SRR1175132

Sample name:

Date: 03-04-2023 03:38:13

Number of reads: 1796251

Percentage reads mapped: 76.16

Strain: lineage3

Drug-resistance: HR-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 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
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
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 9047 c.1746C>T synonymous_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 0.24
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 0.91
rpoB 760490 c.684C>T synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoB 762911 p.Ile1035Met missense_variant 0.12
rpoC 762917 c.-453C>G upstream_gene_variant 0.17
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoC 762929 c.-441G>C upstream_gene_variant 0.17
rpoB 762939 p.Met1045Leu missense_variant 0.12
rpoB 762942 p.Ile1046Val missense_variant 0.11
rpoC 762965 c.-405T>C upstream_gene_variant 0.15
rpoC 762989 c.-381G>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.12
rpoC 763886 c.517C>A synonymous_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 0.15
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 1417155 p.Pro65Ser missense_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.13
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.15
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.14
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.15
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.23
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.23
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.23
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.24
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.28
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.21
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.21
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.21
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.18
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
PPE35 2169320 p.Leu431Phe missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.92
pncA 2289365 c.-125delC upstream_gene_variant 0.91
ahpC 2726105 c.-88G>A upstream_gene_variant 0.95
ahpC 2726587 p.Asp132Gly missense_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.92
panD 4043912 p.Val124Met missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244350 p.Leu373Pro missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407956 p.Arg83Gly missense_variant 0.94