TB-Profiler result

Run: SRR3732568
Summary

Run ID: SRR3732568

Sample name:

Date: 04-04-2023 05:35:43

Number of reads: 1742752

Percentage reads mapped: 99.58

Strain: lineage2.2.1

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
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
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 6089 p.Gly284Trp missense_variant 0.12
gyrB 6290 c.1051C>A synonymous_variant 0.13
gyrB 6489 p.Arg417His missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7838 c.537C>T synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9405 p.Gly702Cys missense_variant 0.14
gyrA 9661 p.Ala787Glu missense_variant 0.15
fgd1 491416 p.Arg212* stop_gained 0.15
fgd1 491507 p.Ala242Glu missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760721 c.915C>A synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763623 p.Ala85Asp missense_variant 0.14
rpoC 765498 p.Ala710Asp missense_variant 0.11
rpoC 766061 p.Val898Phe missense_variant 0.14
rpoC 766453 c.3084G>T synonymous_variant 0.15
rpoC 766462 c.3093G>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
mmpL5 776969 c.1512G>A synonymous_variant 0.13
mmpL5 778429 p.His18Asp missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
mmpS5 779640 c.-735G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781796 p.Met79Ile missense_variant 0.17
rplC 800676 c.-133C>A upstream_gene_variant 0.17
rplC 800961 p.Gln51His missense_variant 0.12
Rv1258c 1406659 p.Leu228Ile missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407317 c.24G>A synonymous_variant 0.15
embR 1417145 p.Ala68Glu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474781 n.1124C>A non_coding_transcript_exon_variant 0.18
rrl 1474790 n.1133C>A non_coding_transcript_exon_variant 0.17
rrl 1475222 n.1565G>T non_coding_transcript_exon_variant 0.2
rpsA 1833703 p.Asp54Glu missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917833 c.-107G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103089 c.-47C>G upstream_gene_variant 0.12
ndh 2103161 c.-119G>T upstream_gene_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155548 c.564C>A synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.18
PPE35 2168124 p.Gly830Val missense_variant 0.12
PPE35 2169057 p.Pro519Gln missense_variant 0.22
PPE35 2169065 c.1548G>C synonymous_variant 0.22
Rv1979c 2221988 p.Leu393Ile missense_variant 0.14
Rv1979c 2222388 c.777G>T synonymous_variant 0.13
Rv1979c 2222780 p.Asp129Asn missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987033 c.195C>A synonymous_variant 0.25
Rv2752c 3065566 p.Pro209His missense_variant 0.14
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0
thyX 3067923 p.Arg8Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448379 c.-125G>T upstream_gene_variant 0.12
Rv3083 3449069 p.Ala189Glu missense_variant 0.14
Rv3083 3449538 c.1035G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474315 c.309C>T synonymous_variant 0.14
whiB7 3568525 p.Cys52Phe missense_variant 0.15
Rv3236c 3612404 p.Ala238Glu missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613192 c.-76G>T upstream_gene_variant 0.14
Rv3236c 3613204 c.-88G>T upstream_gene_variant 0.14
fbiA 3640582 p.Arg14Ser missense_variant 0.13
fbiA 3641413 p.His291Asn missense_variant 0.12
rpoA 3877802 p.Pro236Ala missense_variant 0.1
clpC1 4039498 p.Ile403Val missense_variant 0.11
embC 4241651 c.1791delC frameshift_variant 0.14
embC 4241821 c.1959G>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244525 c.1293G>A synonymous_variant 0.12
embA 4244981 c.1749G>T synonymous_variant 0.14
embA 4245464 p.Asp744Glu missense_variant 0.22
embB 4245947 c.-567C>T upstream_gene_variant 0.13
embB 4249638 p.Leu1042Pro missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267914 p.Pro308Gln missense_variant 0.33
aftB 4268518 p.Ala107Ser missense_variant 0.13
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