TB-Profiler result

Run: SRR5818669
Summary

Run ID: SRR5818669

Sample name:

Date: 04-04-2023 11:41:43

Number of reads: 739426

Percentage reads mapped: 90.91

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 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
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_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 8668 p.Ala456Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761570 c.1764T>C synonymous_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763043 c.-327G>C upstream_gene_variant 0.12
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472056 n.211G>A non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.11
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.18
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.14
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474765 n.1108A>G non_coding_transcript_exon_variant 0.17
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.17
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.25
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.17
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.15
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.31
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.17
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.15
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.31
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.11
rrl 1474826 n.1169T>C non_coding_transcript_exon_variant 0.11
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.26
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.26
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.26
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.24
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.18
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.17
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.22
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.25
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.29
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.29
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.4
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.29
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.29
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.25
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.22
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.22
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.2
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
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
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169349 p.Phe422Leu missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222398 p.Ile256Thr missense_variant 1.0
Rv1979c 2223132 c.33C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_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
clpC1 4039480 p.Arg409Gly missense_variant 0.57
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246553 c.40C>A synonymous_variant 0.4
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
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys 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 4407742 p.Arg154Pro missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0