TB-Profiler result

Run: SRR16295789
Summary

Run ID: SRR16295789

Sample name:

Date: 03-04-2023 17:04:28

Number of reads: 5436356

Percentage reads mapped: 75.88

Strain: lineage2.2.1

Drug-resistance: Other

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 1.0
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575349 c.2T>A start_lost 0.11
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576172 c.825G>A synonymous_variant 0.11
ccsA 620634 c.744C>T synonymous_variant 0.15
ccsA 620660 p.Arg257His missense_variant 0.13
rpoB 761861 c.2055C>T synonymous_variant 0.13
rpoB 762940 p.Met1045Arg missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763379 p.Val4Ile missense_variant 0.11
rpoC 764210 p.Ile281Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777635 c.846C>A synonymous_variant 0.13
mmpL5 778678 c.-198C>A upstream_gene_variant 0.11
mmpR5 779414 p.Leu142Arg missense_variant 1.0
mmpL5 779466 c.-986C>T upstream_gene_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781862 c.303G>T synonymous_variant 0.12
fbiC 1303961 p.Arg344Gln missense_variant 0.11
fbiC 1304070 c.1140C>G synonymous_variant 0.12
fbiC 1304360 p.Arg477Leu missense_variant 0.14
fbiC 1304863 p.Ser645Gly missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416399 p.Asp317Asn missense_variant 0.12
embR 1416888 p.Arg154Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472488 n.643T>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.16
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.19
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.22
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.21
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.22
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.25
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.25
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472701 n.856T>G non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.2
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.22
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.18
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.13
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.22
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.23
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.21
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.21
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.21
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.22
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.21
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.21
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.21
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.21
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.2
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.19
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.28
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.27
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.31
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.31
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.31
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.31
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.28
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.56
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.56
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.55
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.51
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.35
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.33
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.28
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.27
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.27
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.25
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.23
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.21
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.21
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.23
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.21
inhA 1673401 c.-801G>A upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834646 p.Tyr369His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154114 c.1998C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168955 p.Phe553Ser missense_variant 0.12
PPE35 2169032 c.1581T>C synonymous_variant 0.11
PPE35 2170035 p.Val193Ala missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289432 c.-191C>T upstream_gene_variant 0.12
pncA 2289558 c.-317C>T upstream_gene_variant 0.17
kasA 2518348 c.234A>T synonymous_variant 0.14
eis 2715467 c.-135A>G upstream_gene_variant 1.0
eis 2715502 c.-170C>T upstream_gene_variant 0.14
folC 2746721 p.Leu293Pro missense_variant 0.12
thyX 3067306 p.Glu214Lys missense_variant 0.14
thyX 3067482 p.Ala155Val missense_variant 0.13
thyX 3067871 p.Trp25Cys missense_variant 0.14
thyX 3068064 c.-119G>A upstream_gene_variant 0.12
thyA 3073880 p.Glu198* stop_gained 0.12
thyA 3074492 c.-21T>C upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339047 c.-70delC upstream_gene_variant 0.12
fbiD 3339196 c.83delC frameshift_variant 0.13
Rv3083 3448643 p.Leu47Ser missense_variant 0.11
Rv3083 3449915 p.Lys471Arg missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474509 p.Thr168Ile missense_variant 0.12
fprA 3475363 p.Ile453Val missense_variant 0.1
whiB7 3568742 c.-63C>T upstream_gene_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiB 3642641 c.1107G>A synonymous_variant 0.11
alr 3841185 p.Gln79Arg missense_variant 0.14
rpoA 3878559 c.-52G>C upstream_gene_variant 0.22
rpoA 3878590 c.-83G>C upstream_gene_variant 0.15
ddn 3987206 c.363A>G synonymous_variant 0.1
clpC1 4038641 c.2064C>T synonymous_variant 0.11
clpC1 4038794 p.Ser637Arg missense_variant 0.12
clpC1 4039739 c.966C>T synonymous_variant 0.12
clpC1 4040249 p.Glu152Asp missense_variant 0.25
embA 4242271 c.-962A>G upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243086 p.Leu1075Pro missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243868 c.636G>A synonymous_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247074 c.561G>T synonymous_variant 0.11
aftB 4267199 p.Trp546* stop_gained 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268203 c.634C>T synonymous_variant 0.15
ubiA 4269155 p.Thr227Pro missense_variant 0.17
aftB 4269813 c.-977T>C upstream_gene_variant 0.11
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethA 4326680 p.Leu265Pro missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407648 c.555T>C synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0