TB-Profiler result

Run: SRR3675533
Summary

Run ID: SRR3675533

Sample name:

Date: 04-04-2023 05:32:32

Number of reads: 382918

Percentage reads mapped: 93.08

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7501 p.Asp67Gly missense_variant 0.22
gyrA 7504 c.204_208delCAGCC frameshift_variant 0.22
gyrA 7518 c.217_218insGGCTG frameshift_variant 0.22
gyrA 7522 p.Ala74Val missense_variant 0.2
gyrA 7527 p.Ser76Ala missense_variant 0.2
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 575188 c.-160G>T upstream_gene_variant 0.29
ccsA 619831 c.-60T>G upstream_gene_variant 0.38
ccsA 620537 p.Val216Gly missense_variant 0.4
rpoB 760997 c.1191G>T synonymous_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764636 p.Asp423Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775648 p.Gln945Lys missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.15
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.16
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.16
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.17
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.14
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.13
rrl 1476023 n.2366C>T non_coding_transcript_exon_variant 0.14
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.13
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.13
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.14
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.13
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.13
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.13
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.13
rrl 1476076 n.2419A>G non_coding_transcript_exon_variant 0.14
rrl 1476079 n.2422G>A non_coding_transcript_exon_variant 0.13
rrl 1476088 n.2431A>G non_coding_transcript_exon_variant 0.1
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.1
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.12
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.11
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.18
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.13
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.25
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.24
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.19
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.17
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rrl 1476308 n.2651G>T non_coding_transcript_exon_variant 0.13
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.15
rrl 1476519 n.2862C>T non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.17
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.21
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.21
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.21
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
rpsA 1834135 c.594G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.65
PPE35 2170159 p.Ala152Ser missense_variant 0.12
Rv1979c 2222418 p.Asp249Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289994 c.-753A>T upstream_gene_variant 0.25
kasA 2518151 p.Ser13Arg missense_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.13
ald 3087611 c.792G>A synonymous_variant 0.15
fbiD 3339273 c.156T>G synonymous_variant 0.2
Rv3083 3449964 c.1461A>C synonymous_variant 0.13
Rv3083 3449982 c.1479G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568604 p.Asp26Asn missense_variant 0.22
fbiB 3642503 c.969T>C synonymous_variant 1.0
fbiB 3642531 p.Arg333Ser missense_variant 0.22
clpC1 4039484 c.1221T>G synonymous_variant 0.33
panD 4044159 c.123C>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247542 c.1029C>A synonymous_variant 0.18
aftB 4269051 c.-215C>T upstream_gene_variant 1.0
ethA 4326486 p.Gly330Ser missense_variant 0.13
ethA 4327191 p.Asp95His missense_variant 0.15
ethR 4327249 c.-300G>T upstream_gene_variant 0.18
ethR 4327678 p.Asp44Tyr missense_variant 0.18
ethR 4328188 p.Glu214* stop_gained 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0