TB-Profiler result

Run: SRR6045086
Summary

Run ID: SRR6045086

Sample name:

Date: 04-04-2023 11:52:29

Number of reads: 599437

Percentage reads mapped: 87.74

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
gyrB 6242 p.Arg335Cys missense_variant 0.12
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 491599 p.Asp273His missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576369 p.Arg341Pro missense_variant 0.12
rpoB 760561 c.757_758delCG frameshift_variant 0.12
rpoB 760611 c.805T>C synonymous_variant 0.13
rpoB 760634 c.828T>C synonymous_variant 0.15
rpoB 760646 c.840C>G synonymous_variant 0.12
rpoB 760655 c.849A>G synonymous_variant 0.12
rpoB 760661 c.855A>C synonymous_variant 0.13
rpoB 760668 p.Thr288Ala missense_variant 0.13
rpoB 760674 c.868T>C synonymous_variant 0.13
rpoB 760679 c.873A>G synonymous_variant 0.13
rpoB 760683 c.877T>C synonymous_variant 0.12
rpoB 761417 c.1611G>A synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763262 c.-108C>T upstream_gene_variant 0.11
rpoC 765283 c.1914C>G synonymous_variant 0.12
rpoC 765288 p.Leu640Gln missense_variant 0.12
rpoC 765292 c.1923G>T synonymous_variant 0.12
rpoC 765300 p.Val644Ala missense_variant 0.12
rpoC 765305 p.Ile646Val missense_variant 0.12
rpoC 765319 c.1950A>G synonymous_variant 0.11
rpoC 765323 c.1955_1957delGCC disruptive_inframe_deletion 0.12
rpoC 765330 p.Ser654Asn missense_variant 0.11
rpoC 765343 c.1974G>A synonymous_variant 0.12
rpoC 765352 c.1983G>C synonymous_variant 0.12
rpoC 765356 p.Met663Val missense_variant 0.12
rpoC 765379 c.2010G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpR5 779162 p.Thr58Met missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.12
Rv1258c 1406088 p.Ala418Asp missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.29
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.29
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.29
rrl 1474743 n.1086T>G non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 1.0
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 1.0
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 1.0
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 1.0
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 1.0
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 1.0
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 1.0
rrl 1475220 n.1563G>T non_coding_transcript_exon_variant 1.0
rrl 1475240 n.1583C>G non_coding_transcript_exon_variant 1.0
fabG1 1673371 c.-69T>G upstream_gene_variant 0.12
rpsA 1834664 p.Pro375Thr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918336 p.Arg133Trp missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155986 c.126G>A synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170188 p.Glu142Leu missense_variant 0.14
Rv1979c 2222118 c.1047G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714809 p.Phe175Ser missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.33
Rv2752c 3065508 c.683delG frameshift_variant 0.15
Rv2752c 3065678 p.Lys172* stop_gained 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642098 c.564G>A synonymous_variant 1.0
alr 3840636 p.Pro262Gln missense_variant 1.0
alr 3841515 c.-95C>A upstream_gene_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3878567 c.-60C>G upstream_gene_variant 0.4
rpoA 3878622 c.-115C>G upstream_gene_variant 1.0
clpC1 4038890 c.1815G>A synonymous_variant 0.11
clpC1 4038896 c.1809C>A synonymous_variant 0.11
clpC1 4039003 p.Asn568Asp missense_variant 0.2
clpC1 4039745 c.960C>T synonymous_variant 0.15
clpC1 4039751 c.954A>G synonymous_variant 0.14
clpC1 4039814 c.891C>G synonymous_variant 0.11
clpC1 4039831 c.874T>C synonymous_variant 0.13
clpC1 4039850 c.855T>C synonymous_variant 0.14
clpC1 4039865 c.840T>C synonymous_variant 0.2
clpC1 4039874 c.831C>T synonymous_variant 0.16
clpC1 4039904 c.801A>G synonymous_variant 0.15
clpC1 4039907 c.798G>A synonymous_variant 0.21
clpC1 4039931 c.774T>C synonymous_variant 0.18
clpC1 4039934 c.771G>C synonymous_variant 0.17
clpC1 4039943 c.762G>C synonymous_variant 0.17
clpC1 4039946 c.759A>G synonymous_variant 0.16
clpC1 4039949 c.756G>C synonymous_variant 0.16
clpC1 4039952 c.753T>C synonymous_variant 0.16
clpC1 4039958 c.747G>C synonymous_variant 0.15
clpC1 4039964 c.741C>G synonymous_variant 0.14
clpC1 4039975 p.Asp244Asn missense_variant 0.13
clpC1 4039979 c.726C>G synonymous_variant 0.1
clpC1 4039982 c.723G>A synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245883 p.Gly884Asp missense_variant 1.0
embB 4246871 p.Ala120Thr missense_variant 0.14
embB 4249745 p.Leu1078Phe missense_variant 0.22
embB 4249749 p.Glu1079Val missense_variant 0.22
ethA 4326230 p.Asp415Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0