TB-Profiler result

Run: ERR4815400
Summary

Run ID: ERR4815400

Sample name:

Date: 01-04-2023 13:50:34

Number of reads: 779815

Percentage reads mapped: 90.44

Strain: lineage1.1.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 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 1472733 n.888G>A non_coding_transcript_exon_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
gyrB 5239 c.-1C>A upstream_gene_variant 0.17
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7307 c.6A>G synonymous_variant 0.12
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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9661 p.Ala787Val missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.92
rpoB 760038 p.Gly78Cys missense_variant 0.29
rpoB 761609 p.Met601Ile missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775913 c.2568C>A synonymous_variant 0.2
mmpL5 775948 p.Ala845Ser missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303251 c.321C>T synonymous_variant 0.13
fbiC 1303290 p.Ser120Arg missense_variant 0.13
Rv1258c 1406517 p.Ala275Gly missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460930 c.-115C>A upstream_gene_variant 0.13
atpE 1461227 c.183G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.67
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.67
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.67
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.75
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.75
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.77
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.8
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.83
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.89
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.83
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.37
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.89
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.89
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.89
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.75
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.93
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.93
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.93
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.93
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.92
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.75
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrl 1474974 n.1317G>A non_coding_transcript_exon_variant 1.0
inhA 1674267 c.66G>T synonymous_variant 0.12
rpsA 1834319 p.Val260Ile missense_variant 1.0
rpsA 1834351 p.Glu270Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918571 p.Val211Ala missense_variant 0.1
ndh 2101949 p.Phe365Ser missense_variant 0.17
ndh 2102759 p.Ala95Asp missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518021 c.-94A>G upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518433 p.Arg107Trp missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726070 c.-123G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067501 c.444delC frameshift_variant 0.12
thyA 3073965 c.507C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087124 p.Ala102Val missense_variant 0.11
ald 3087653 c.834A>G synonymous_variant 0.17
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 3475128 c.1123dupG frameshift_variant 0.11
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4039022 c.1683A>G synonymous_variant 0.2
clpC1 4040030 c.675C>T synonymous_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040607 p.Ile33Thr missense_variant 0.22
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 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268725 p.Val38Leu missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327483 c.-10G>A upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu 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 4407612 c.580_590delAACTATTTGCG frameshift_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407964 p.Ala80Glu missense_variant 0.12