TB-Profiler result

Run: SRR1173812
Summary

Run ID: SRR1173812

Sample name:

Date: 03-04-2023 03:32:18

Number of reads: 1483595

Percentage reads mapped: 97.54

Strain: lineage3

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
lineage3 East-African-Indian CAS 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
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 5899 p.Asp220Glu missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7759 c.461dupC frameshift_variant 0.14
gyrA 7777 p.Arg159Gln missense_variant 0.14
gyrA 8131 p.Gln277Arg missense_variant 1.0
gyrA 9077 c.1779dupG frameshift_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491034 c.252C>T synonymous_variant 0.13
fgd1 491281 p.Asp167Asn missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760375 p.Asp190Val missense_variant 0.12
rpoB 761027 c.1221A>T synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762669 p.Asp955Tyr missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775758 p.Thr908Asn missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781575 p.Gln6* stop_gained 0.13
rplC 801362 p.Val185Asp missense_variant 0.11
Rv1258c 1406375 c.966C>A synonymous_variant 0.11
Rv1258c 1407102 p.Ala80Val missense_variant 0.22
Rv1258c 1407433 c.-93A>T upstream_gene_variant 0.17
Rv1258c 1407443 c.-103C>G upstream_gene_variant 0.22
Rv1258c 1407444 c.-104T>G upstream_gene_variant 0.22
Rv1258c 1407450 c.-111_-110insA upstream_gene_variant 0.22
embR 1416570 c.778C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473951 n.294G>A non_coding_transcript_exon_variant 0.15
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.12
rrl 1474183 n.526T>A non_coding_transcript_exon_variant 0.14
inhA 1673580 c.-622T>A upstream_gene_variant 0.13
inhA 1674270 p.Phe23Leu missense_variant 0.12
inhA 1674879 c.678T>G synonymous_variant 0.17
rpsA 1833410 c.-132G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918488 c.549G>A synonymous_variant 0.13
ndh 2102636 p.Pro136Leu missense_variant 0.12
katG 2153999 p.Arg705Trp missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518589 p.Gly159Arg missense_variant 0.12
kasA 2518605 p.Val164Glu missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746175 p.Ala475Val missense_variant 0.15
ribD 2986799 c.-40G>T upstream_gene_variant 0.12
Rv2752c 3064596 c.1596G>A synonymous_variant 0.4
Rv2752c 3065565 c.627C>A synonymous_variant 0.12
Rv2752c 3066204 c.-14_-13insA upstream_gene_variant 0.2
thyX 3067321 p.Arg209Trp missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087396 p.Thr193Ser missense_variant 1.0
fbiD 3339307 p.Pro64Ser missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474170 p.Pro55Gln missense_variant 0.12
whiB7 3568737 c.-58C>T upstream_gene_variant 0.12
fbiB 3641542 c.12delC frameshift_variant 0.11
alr 3840486 p.Ile312Asn missense_variant 0.11
clpC1 4040753 c.-49G>A upstream_gene_variant 1.0
embC 4240402 c.540C>T synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245013 p.Arg594Leu missense_variant 0.13
embB 4248387 p.Arg625Gln missense_variant 0.17
aftB 4267498 p.Glu447Lys missense_variant 0.22
ubiA 4269893 c.-60G>T upstream_gene_variant 0.17
ethR 4326610 c.-939G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0