TB-Profiler result

Run: ERR4817448
Summary

Run ID: ERR4817448

Sample name:

Date: 01-04-2023 14:59:56

Number of reads: 420003

Percentage reads mapped: 99.36

Strain: lineage6.3.1

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
lineage6 West-Africa 2 AFRI_1 RD702 1.0
lineage6.3 West-Africa 2 AFRI_1 RD702 1.0
lineage6.3.1 West-Africa 2 AFRI_1 RD702 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
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 6446 p.Ala403Ser missense_variant 1.0
gyrB 6464 p.Lys409Gln missense_variant 0.14
gyrA 7322 c.21G>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7629 p.Val110Met missense_variant 0.22
gyrA 8530 p.Ala410Val missense_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9789 p.Ala830Ser missense_variant 0.29
fgd1 491668 p.Lys296Glu missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761548 p.Val581Ala missense_variant 0.12
rpoB 761674 p.Gly623Val missense_variant 0.2
rpoB 761723 p.Glu639Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764444 p.Asp359Tyr missense_variant 0.14
rpoC 764953 c.1584G>T synonymous_variant 0.12
rpoC 766599 p.Tyr1077Ser missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776305 p.Pro726Ser missense_variant 0.29
mmpL5 776546 p.Met645Ile missense_variant 0.2
mmpR5 778154 c.-836G>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800780 c.-29C>T upstream_gene_variant 0.15
rplC 801453 c.645T>C synonymous_variant 0.22
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303018 c.88C>T synonymous_variant 0.14
embR 1417023 p.Thr109Ser missense_variant 0.4
atpE 1461251 c.207G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472608 n.767delG non_coding_transcript_exon_variant 0.17
rrs 1473174 n.1329G>A non_coding_transcript_exon_variant 0.12
rrl 1474421 n.764G>T non_coding_transcript_exon_variant 0.25
rrl 1474549 n.892G>T non_coding_transcript_exon_variant 0.12
fabG1 1673392 c.-48G>C upstream_gene_variant 0.18
inhA 1674434 p.Val78Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102694 p.Val117Ile missense_variant 1.0
katG 2154128 p.Leu662Phe missense_variant 0.13
katG 2154562 p.Val517Ala missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155080 c.1032G>A synonymous_variant 0.25
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156550 c.-439G>C upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169593 c.1020C>T synonymous_variant 0.25
PPE35 2169752 c.861C>T synonymous_variant 0.33
Rv1979c 2221932 c.1233G>T synonymous_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518077 c.-38G>A upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518140 p.Gly9Val missense_variant 0.13
eis 2714603 p.Val244Ile missense_variant 0.13
ribD 2987179 p.Val114Asp missense_variant 0.25
Rv2752c 3064671 c.1521C>T synonymous_variant 1.0
Rv2752c 3065024 p.Pro390Ser missense_variant 0.25
Rv2752c 3065905 p.Leu96Arg missense_variant 0.13
thyX 3067939 p.Glu3* stop_gained 0.2
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087228 p.Ala137Thr missense_variant 0.22
ald 3087725 c.906C>A synonymous_variant 0.12
Rv3083 3448833 c.330G>A synonymous_variant 0.29
Rv3083 3449195 p.Gly231Asp missense_variant 0.18
Rv3083 3449781 c.1278G>A synonymous_variant 1.0
fprA 3473963 c.-44G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612969 p.Gly50Trp missense_variant 0.15
fbiA 3640492 c.-51G>T upstream_gene_variant 0.14
alr 3840610 p.Leu271Met missense_variant 0.29
rpoA 3877629 c.879C>T synonymous_variant 0.15
rpoA 3877696 p.Thr271Ile missense_variant 1.0
rpoA 3878052 c.456C>T synonymous_variant 0.33
ddn 3986704 c.-140C>A upstream_gene_variant 0.2
ddn 3986985 p.Leu48Met missense_variant 0.17
clpC1 4038816 p.Ala630Glu missense_variant 0.13
clpC1 4039040 c.1665C>A synonymous_variant 0.22
clpC1 4040166 p.Ala180Val missense_variant 0.18
clpC1 4040365 c.340C>A synonymous_variant 0.18
panD 4043985 c.297C>T synonymous_variant 0.18
embC 4240002 p.Thr47Ile missense_variant 0.15
embC 4240313 p.Thr151Ala missense_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241658 p.Ser599* stop_gained 0.18
embC 4241843 p.Leu661Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242946 c.-287T>C upstream_gene_variant 0.25
embA 4243213 c.-20G>A upstream_gene_variant 0.22
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 1.0
embA 4244821 p.Gly530Ala missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249516 c.3003G>A synonymous_variant 0.13
aftB 4268345 c.492C>A synonymous_variant 0.5
aftB 4268477 c.360C>T synonymous_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326331 c.1143C>A synonymous_variant 0.15
ethA 4326465 p.Ile337Val missense_variant 1.0
whiB6 4338592 c.-71G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408306 c.-104C>T upstream_gene_variant 0.25