TB-Profiler result

Run: ERR1577250
Summary

Run ID: ERR1577250

Sample name:

Date: 31-03-2023 14:39:42

Number of reads: 1007496

Percentage reads mapped: 98.73

Strain: lineage2.2.1

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
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
rpsL 781687 p.Lys43Arg missense_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
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 1.0
ccsA 619881 c.-10G>T upstream_gene_variant 0.18
ccsA 619999 c.112delC frameshift_variant 0.11
ccsA 620187 c.297C>A synonymous_variant 0.2
ccsA 620192 p.Ala101Asp missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620757 p.Asp289Glu missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoB 761162 c.1356G>T synonymous_variant 0.24
rpoB 761710 p.Val635Asp missense_variant 0.25
rpoB 761713 p.Val636Asp missense_variant 0.25
rpoB 761778 p.Asn658Asp missense_variant 0.17
rpoB 762101 c.2295C>G synonymous_variant 0.11
rpoB 762219 p.Glu805Gln missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764336 p.Glu323Gln missense_variant 0.12
rpoC 764680 p.Lys437Asn missense_variant 0.16
rpoC 766499 p.Ala1044Pro missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776224 p.Gly753* stop_gained 0.15
mmpL5 777606 p.Gly292Val missense_variant 0.29
mmpL5 778462 p.Ala7Ser missense_variant 0.19
mmpR5 779190 p.Ile67Met missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801276 c.470delC frameshift_variant 0.15
fbiC 1304551 p.Gly541Cys missense_variant 0.25
fbiC 1304801 p.Arg624Leu missense_variant 0.15
fbiC 1305501 c.2571G>C stop_lost&splice_region_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407156 p.Ala62Asp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472955 n.1110C>A non_coding_transcript_exon_variant 0.15
rrs 1473319 n.1474C>A non_coding_transcript_exon_variant 0.17
rrl 1473479 n.-179G>T upstream_gene_variant 0.2
rrl 1473539 n.-119C>G upstream_gene_variant 0.11
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.17
rrl 1474096 n.439C>A non_coding_transcript_exon_variant 0.22
rrl 1474097 n.440C>A non_coding_transcript_exon_variant 0.22
rrl 1474719 n.1062G>T non_coding_transcript_exon_variant 0.14
rrl 1474746 n.1089G>T non_coding_transcript_exon_variant 0.22
rrl 1475754 n.2097G>T non_coding_transcript_exon_variant 0.27
rrl 1475788 n.2131C>A non_coding_transcript_exon_variant 0.18
rrl 1475906 n.2249C>G non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.94
rpsA 1834226 p.Gly229Cys missense_variant 0.17
rpsA 1834891 c.1350G>T synonymous_variant 0.17
rpsA 1834943 p.Ala468Ser missense_variant 0.27
rpsA 1834956 p.Ala472Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102313 p.Gln244Glu missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154825 c.1287G>C synonymous_variant 0.12
katG 2155334 p.Val260Leu missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170136 c.476delC frameshift_variant 0.15
Rv1979c 2222066 p.Leu367Val missense_variant 0.11
Rv1979c 2222532 c.633C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518717 c.603C>A synonymous_variant 0.17
kasA 2518886 p.Gly258Arg missense_variant 0.12
kasA 2518967 p.Val285Phe missense_variant 0.14
kasA 2519003 p.Leu297Met missense_variant 0.15
kasA 2519026 p.Asp304Glu missense_variant 0.18
kasA 2519215 c.1105_1107delCCG conservative_inframe_deletion 0.2
kasA 2519327 p.Gly405Arg missense_variant 0.12
eis 2714985 c.348G>C synonymous_variant 0.12
eis 2715501 c.-169G>C upstream_gene_variant 0.11
ahpC 2726499 p.Leu103Val missense_variant 0.11
folC 2746231 c.1368G>C synonymous_variant 0.11
folC 2747703 c.-105C>G upstream_gene_variant 0.1
pepQ 2859482 p.Ala313Pro missense_variant 0.14
pepQ 2860122 p.Ser99Arg missense_variant 0.17
pepQ 2860136 p.Leu95Met missense_variant 0.17
Rv2752c 3065500 p.Gly231Val missense_variant 0.89
thyX 3067326 p.Glu207Gly missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339525 c.408G>T synonymous_variant 0.19
fbiD 3339696 c.579C>A synonymous_variant 0.2
Rv3083 3448307 c.-197T>C upstream_gene_variant 0.11
Rv3083 3448887 c.384C>A synonymous_variant 0.24
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612520 c.597G>C synonymous_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642044 c.510G>T synonymous_variant 0.14
fbiB 3642233 c.700delC frameshift_variant 0.14
fbiB 3642258 p.Trp242Arg missense_variant 0.17
clpC1 4039550 c.1155G>C synonymous_variant 0.11
panD 4043878 c.403delC frameshift_variant 0.13
embC 4241062 c.1200G>T synonymous_variant 0.19
embC 4241069 p.Ala403Ser missense_variant 0.17
embC 4241113 c.1251G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242697 p.Leu945Phe missense_variant 0.11
embA 4243387 p.Asp52Ala missense_variant 0.12
embA 4243453 c.225delC frameshift_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246462 p.Gly1077Val missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246821 p.Pro103His missense_variant 0.16
embB 4247043 p.Pro177Arg missense_variant 0.1
embB 4247886 p.Gly458Val missense_variant 0.15
embB 4248881 p.Pro790Thr missense_variant 0.28
embB 4249317 p.Ala935Asp missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327543 c.-70C>A upstream_gene_variant 0.17
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