TB-Profiler result

Run: SRR16295732
Summary

Run ID: SRR16295732

Sample name:

Date: 03-04-2023 16:59:57

Number of reads: 6155390

Percentage reads mapped: 85.45

Strain: lineage2.2.1

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
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 0.12 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
gyrB 6591 p.Arg451Leu 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575376 p.Ser10Leu missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.65
mshA 576111 p.Ala255Gly missense_variant 0.3
mshA 576482 p.Val379Leu missense_variant 0.38
rpoB 762457 p.Gly884Asp missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766380 p.Gly1004Asp missense_variant 0.13
rpoC 766812 p.Ser1148* stop_gained 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777064 p.Phe473Leu missense_variant 0.11
mmpL5 777235 p.Asn416His missense_variant 0.19
mmpL5 777398 c.1083G>A synonymous_variant 0.14
mmpL5 777432 p.Ala350Glu missense_variant 0.18
mmpR5 779273 c.286_287dupCG frameshift_variant 0.95
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Ala missense_variant 0.25
fbiC 1304369 p.Val480Glu missense_variant 0.17
fbiC 1305125 p.Arg732His missense_variant 0.12
fbiC 1305470 p.Arg847Leu missense_variant 0.13
Rv1258c 1406358 p.Ile328Thr missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417064 p.Ala95Val missense_variant 0.18
embR 1417261 c.87A>G synonymous_variant 0.12
embR 1417268 p.Pro27Gly missense_variant 0.13
embR 1417276 c.72C>T synonymous_variant 0.14
embR 1417408 c.-61A>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.11
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrs 1473048 n.1203T>C non_coding_transcript_exon_variant 0.1
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.2
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.19
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.21
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.26
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.24
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.16
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.15
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.15
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.15
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.15
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.16
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.16
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.2
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.2
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.24
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.34
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.31
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.18
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.18
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.19
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.19
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.19
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.18
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.21
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.24
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.21
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.21
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.21
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.17
fabG1 1673452 p.Ala5Ser missense_variant 0.15
fabG1 1673461 p.Gly8Trp missense_variant 0.12
inhA 1673556 c.-646C>T upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834984 c.1443T>C synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918184 p.Ala82Val missense_variant 0.13
tlyA 1918696 p.Ala253Ser missense_variant 0.13
katG 2154650 p.Lys488Glu missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168329 p.Pro762Ser missense_variant 0.12
PPE35 2170030 p.Met195Leu missense_variant 0.11
PPE35 2170035 p.Val193Ala missense_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288722 p.Glu174Lys missense_variant 0.2
pncA 2290228 c.-987G>T upstream_gene_variant 0.12
kasA 2518348 c.234A>T synonymous_variant 0.14
eis 2715467 c.-135A>G upstream_gene_variant 1.0
pepQ 2859596 p.Ala275Thr missense_variant 0.13
Rv2752c 3065190 c.1002C>A synonymous_variant 0.14
Rv2752c 3065711 p.Gly161Ser missense_variant 0.15
thyX 3067377 p.Arg190Leu missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568531 p.Arg50Gln missense_variant 0.12
Rv3236c 3612499 c.618C>T synonymous_variant 0.14
Rv3236c 3612730 c.387C>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612937 c.180C>T synonymous_variant 0.12
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiA 3641280 p.Ile246Met missense_variant 0.11
fbiA 3641333 p.Gly264Ala missense_variant 0.12
fbiA 3641340 p.Asp266Glu missense_variant 0.13
fbiA 3641347 p.Ala269Pro missense_variant 0.14
fbiB 3642230 c.696G>T synonymous_variant 0.12
alr 3840231 p.Arg397His missense_variant 0.18
rpoA 3878415 c.93C>T synonymous_variant 0.12
rpoA 3878567 c.-60C>G upstream_gene_variant 0.2
rpoA 3878599 c.-92C>G upstream_gene_variant 0.29
rpoA 3878609 c.-102T>A upstream_gene_variant 0.22
rpoA 3878639 c.-132C>G upstream_gene_variant 0.25
clpC1 4039317 p.Glu463Val missense_variant 0.2
clpC1 4040447 p.Lys86Asn missense_variant 0.12
embC 4241578 c.1716G>T synonymous_variant 0.2
embC 4242287 p.Leu809Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242731 p.Trp957Arg missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244086 p.Pro285Gln missense_variant 0.12
embA 4244291 c.1059G>A synonymous_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.23
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.21
embB 4246822 c.309C>A synonymous_variant 0.14
embB 4247024 p.Pro171Ala missense_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269072 c.-236G>A upstream_gene_variant 0.12
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethA 4327275 p.Arg67Cys missense_variant 0.14
ethA 4327836 c.-363G>A upstream_gene_variant 0.14
ethR 4327843 p.Arg99Cys missense_variant 0.14
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