TB-Profiler result

Run: SRR11972306
Summary

Run ID: SRR11972306

Sample name:

Date: 03-04-2023 05:36:31

Number of reads: 2317672

Percentage reads mapped: 94.4

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Gly missense_variant 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.89 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289225 p.Ile6Thr missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760591 p.Val262Ala missense_variant 0.14
rpoB 760611 c.805T>C synonymous_variant 0.14
rpoB 762176 c.2370T>C synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 0.93
rpoC 764635 c.1266C>G synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 765370 c.2001G>C synonymous_variant 0.14
rpoC 765462 p.Asn698Ser missense_variant 0.9
rpoC 765700 c.2331T>C synonymous_variant 0.13
rpoC 765835 c.2466C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.12
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.14
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.12
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.12
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.12
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.12
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.16
rrl 1475201 n.1544G>A non_coding_transcript_exon_variant 0.17
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.17
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.17
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.17
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.19
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.19
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.17
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.16
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.16
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.16
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.16
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.14
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.13
rrl 1475409 n.1752T>C non_coding_transcript_exon_variant 0.13
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.12
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.13
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747437 p.Met54Ile missense_variant 0.97
thyX 3067478 c.468C>T synonymous_variant 0.14
thyX 3067499 c.447G>A synonymous_variant 0.13
thyX 3067504 p.Ala148Thr missense_variant 0.13
thyX 3067515 p.Ser144Thr missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878271 c.237T>C synonymous_variant 0.12
rpoA 3878337 c.171T>C synonymous_variant 0.13
rpoA 3878343 c.165C>G synonymous_variant 0.14
rpoA 3878346 c.162T>C synonymous_variant 0.14
rpoA 3878364 c.144A>T synonymous_variant 0.13
embC 4241958 p.Arg699Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.94
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269310 p.Trp175Ser missense_variant 1.0
whiB6 4338425 p.Val33Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0