TB-Profiler result

Run: SRR14782707
Summary

Run ID: SRR14782707

Sample name:

Date: 03-04-2023 11:36:01

Number of reads: 6764351

Percentage reads mapped: 92.99

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
gid 4408087 c.115delC frameshift_variant 0.98 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 0.99
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 766645 p.Glu1092Asp missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.15
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
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.13
rrs 1472518 n.673G>A non_coding_transcript_exon_variant 0.11
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.14
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.15
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.21
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.2
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.2
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.13
rrs 1472678 n.834_840delTCCTTGG non_coding_transcript_exon_variant 0.13
rrs 1472687 n.842_843insCC non_coding_transcript_exon_variant 0.13
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472698 n.853A>C non_coding_transcript_exon_variant 0.13
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.34
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.35
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.34
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.26
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.23
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.23
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.22
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.22
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.19
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.19
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.11
fabG1 1673553 p.Asp38Glu missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2222112 c.1052dupT frameshift_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.51
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.28
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
rpoA 3878597 c.-90G>C upstream_gene_variant 0.21
rpoA 3878641 c.-134C>G upstream_gene_variant 0.49
embC 4240409 p.Pro183Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.28
embB 4246584 p.Arg24Pro missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.99
ethA 4327406 p.Leu23Arg missense_variant 0.99
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