TB-Profiler result

Run: SRR6797383
Summary

Run ID: SRR6797383

Sample name:

Date: 04-04-2023 16:08:09

Number of reads: 1985104

Percentage reads mapped: 99.55

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.99
lineage3.1.2.1 East-African-Indian CAS2 RD750 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
gid 4408126 p.Leu26* stop_gained 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8904 p.Arg535Gly missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.14
rpoB 759731 c.-76T>C upstream_gene_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.92
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 764397 p.Leu343Gln missense_variant 0.2
rpoC 766882 c.3513C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778024 p.Leu153Phe missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461136 p.Ala31Asp missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473034 n.1189A>G non_coding_transcript_exon_variant 0.17
rrl 1474925 n.1268G>A non_coding_transcript_exon_variant 0.14
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155375 p.Val246Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.95
pncA 2289365 c.-125delC upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ribD 2987466 p.Glu210Gln missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612359 p.Gly253Ala missense_variant 1.0
Rv3236c 3612977 p.Gly47Asp missense_variant 0.13
fbiB 3640626 c.-909T>C upstream_gene_variant 0.11
fbiB 3641364 c.-171G>A upstream_gene_variant 0.11
rpoA 3878297 p.Glu71* stop_gained 0.12
rpoA 3878674 c.-167G>T upstream_gene_variant 0.2
ddn 3986731 c.-114dupT upstream_gene_variant 0.11
clpC1 4039427 p.Glu426Asp missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0