TB-Profiler result

Run: DRR099689
Summary

Run ID: DRR099689

Sample name:

Date: 31-03-2023 07:02:34

Number of reads: 1911121

Percentage reads mapped: 77.14

Strain: lineage1.1.1.1

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
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
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO 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 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
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 0.99
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777581 p.Tyr300* stop_gained 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 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.11
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.97
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.26
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.28
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.35
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.38
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.46
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.47
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.47
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.45
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.36
rrl 1476516 n.2859G>A non_coding_transcript_exon_variant 0.34
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.33
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.33
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.32
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.32
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.32
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.33
rrl 1476532 n.2876_2877insCG non_coding_transcript_exon_variant 0.32
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.33
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.32
rrl 1476588 n.2931A>G non_coding_transcript_exon_variant 0.3
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.28
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.22
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.18
rrl 1476611 n.2954T>C non_coding_transcript_exon_variant 0.16
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.11
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
rrl 1476630 n.2973A>C non_coding_transcript_exon_variant 0.12
rrl 1476645 n.2988A>G non_coding_transcript_exon_variant 0.13
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918230 c.291C>T synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-278G>C upstream_gene_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
pncA 2289249 c.-8G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_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
fbiB 3642852 p.Pro440Ser missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
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 4243848 p.Val206Met missense_variant 0.99
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
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C 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 4407873 c.330G>T synonymous_variant 1.0