TB-Profiler result

Run: SRR17156538
Summary

Run ID: SRR17156538

Sample name:

Date: 03-04-2023 17:54:52

Number of reads: 338068

Percentage reads mapped: 99.51

Strain: La2

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
La2 M.caprae None None 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 5752 c.513G>A synonymous_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 6922 c.-380G>T upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7871 c.570G>T synonymous_variant 0.15
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576178 c.831G>A synonymous_variant 0.2
ccsA 619831 c.-60T>G upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776159 c.2322T>C synonymous_variant 0.14
mmpL5 776839 p.Asp548Asn missense_variant 1.0
mmpL5 778051 p.Gly144Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305248 p.Ala773Val missense_variant 0.12
Rv1258c 1406873 c.468C>G synonymous_variant 0.17
Rv1258c 1407255 p.Ala29Val missense_variant 1.0
embR 1417042 c.306G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 1.0
rrs 1473043 n.1198G>T non_coding_transcript_exon_variant 0.14
rrs 1473284 n.1439A>G non_coding_transcript_exon_variant 0.11
rrl 1474153 n.496C>T non_coding_transcript_exon_variant 0.17
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.17
rrl 1474355 n.698A>T non_coding_transcript_exon_variant 1.0
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.33
inhA 1673766 c.-436C>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102194 p.Ser283Arg missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155291 p.Lys274Thr missense_variant 0.12
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167681 p.Ser978Pro missense_variant 0.14
PPE35 2167907 c.2706A>G synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170149 p.His155Arg missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715035 p.Met100Val missense_variant 1.0
ribD 2987239 p.Thr134Asn missense_variant 0.18
Rv2752c 3065118 c.1074C>T synonymous_variant 1.0
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
Rv3083 3448330 c.-174A>C upstream_gene_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038353 c.2352G>A synonymous_variant 0.25
clpC1 4039569 p.Met379Thr missense_variant 0.12
clpC1 4040241 p.Thr155Ile missense_variant 0.11
clpC1 4040250 p.Glu152Gly missense_variant 0.11
embC 4240508 p.Ala216Thr missense_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>A upstream_gene_variant 1.0
embA 4243779 p.Pro183Thr missense_variant 0.11
embA 4244117 c.885G>T synonymous_variant 0.12
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247602 c.1089G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268008 p.Gly277Arg missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269523 p.Thr104Ile missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327277 p.Phe66Tyr missense_variant 0.12
ethA 4327362 p.Arg38Trp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0