TB-Profiler result

Run: SRR3732690
Summary

Run ID: SRR3732690

Sample name:

Date: 04-04-2023 05:37:46

Number of reads: 1671335

Percentage reads mapped: 99.62

Strain: lineage2.2.1

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 5754 c.517_521dupTTCTG frameshift_variant 0.17
gyrB 6466 p.Lys409Asn missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9664 p.Ala788Glu missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619856 c.-35G>T upstream_gene_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620829 c.939G>T synonymous_variant 0.14
rpoB 761066 c.1260G>T synonymous_variant 0.12
rpoB 761145 p.Arg447Ser missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779023 p.Ala12Ser missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304908 p.Gly660Trp missense_variant 0.12
fbiC 1305004 p.Glu692Lys missense_variant 0.2
fbiC 1305051 c.2121G>T synonymous_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407212 p.Gln43His missense_variant 0.12
Rv1258c 1407453 c.-113C>A upstream_gene_variant 0.11
embR 1417429 c.-82G>A upstream_gene_variant 0.12
atpE 1461115 p.Ala24Asp missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.77G>T non_coding_transcript_exon_variant 0.5
rrl 1473563 n.-95T>A upstream_gene_variant 0.4
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.67
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.4
rrl 1475102 n.1445C>A non_coding_transcript_exon_variant 0.33
fabG1 1673870 p.Ser144Ile missense_variant 0.12
fabG1 1674131 p.Tyr231Cys missense_variant 0.13
rpsA 1833669 p.Ile43Asn missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834522 c.981C>T synonymous_variant 0.13
rpsA 1834553 p.Val338Phe missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102114 p.Ser310Tyr missense_variant 0.12
ndh 2102932 c.111C>T synonymous_variant 0.15
ndh 2102967 c.75delC frameshift_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168327 c.2286G>T synonymous_variant 0.13
Rv1979c 2222640 c.525G>T synonymous_variant 0.22
Rv1979c 2222683 p.Trp161Ser missense_variant 0.18
Rv1979c 2223268 c.-104G>T upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290059 c.-818T>C upstream_gene_variant 0.12
ahpC 2726315 p.Asp41Glu missense_variant 0.12
folC 2746761 p.Gln280Lys missense_variant 0.12
pepQ 2860589 c.-171G>T upstream_gene_variant 0.13
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0
thyX 3067612 p.Lys112* stop_gained 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086981 c.162C>T synonymous_variant 0.12
Rv3083 3448603 p.Leu34Ile missense_variant 0.12
Rv3083 3448730 p.Ala76Asp missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474573 c.567C>T synonymous_variant 0.14
fprA 3475328 p.Arg441Leu missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877710 c.798C>A synonymous_variant 0.17
rpoA 3878424 c.84G>T synonymous_variant 0.22
clpC1 4038768 p.Arg646Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245800 p.Trp856Cys missense_variant 0.12
embB 4249732 c.3219C>A synonymous_variant 0.14
embB 4249805 p.Pro1098Thr missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0