TB-Profiler result

Run: SRR21727888
Summary

Run ID: SRR21727888

Sample name:

Date: 04-04-2023 03:18:22

Number of reads: 1059690

Percentage reads mapped: 96.01

Strain: lineage1.2.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.23 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.18
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.17
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.27
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.25
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.18
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.19
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.14
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.11
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.4
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.44
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.5
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.4
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.4
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.4
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.4
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.4
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.5
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.57
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.56
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.56
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.57
rrl 1474717 n.1060_1061insGGTTC non_coding_transcript_exon_variant 0.5
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 0.5
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.5
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.5
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.57
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.57
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.67
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.67
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.67
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.67
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.67
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.5
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.5
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.5
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.43
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.43
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.43
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.43
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
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 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
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
thyA 3074103 c.369C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3642584 c.1050G>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 0.97
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407949 p.Asp85Gly missense_variant 1.0