TB-Profiler result

Run: SRR13423579

Summary

Run ID: SRR13423579

Sample name:

Date: 03-04-2023 08:53:02

Number of reads: 5979251

Percentage reads mapped: 94.36

Strain: lineage2.2.1

Drug-resistance: RR-TB


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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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 5785 c.546C>A synonymous_variant 0.12
gyrA 6679 c.-623G>A upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7831 p.Gly177Val missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575282 c.-66C>T upstream_gene_variant 1.0
mshA 575657 p.Ala104Ser missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576069 p.Gly241Asp missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762712 c.2907_2908delGG frameshift_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.8
rpoC 765671 p.Asp768Asn missense_variant 0.13
rpoC 765984 c.2617dupC frameshift_variant 0.12
rpoC 766411 c.3044delT frameshift_variant 0.11
rpoC 766559 p.Ile1064Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775684 p.Leu933Ile missense_variant 0.13
mmpL5 775747 p.Met912Leu missense_variant 0.25
mmpL5 775859 p.Met874Ile missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.91
mmpL5 776960 c.1521C>T synonymous_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781756 p.Tyr66Ser missense_variant 0.29
fbiC 1303821 c.891C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.25
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.2
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.29
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.22
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.3
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.36
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.58
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.44
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.44
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.44
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.44
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.44
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.44
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.44
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.57
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.57
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.57
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.57
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.56
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.47
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.44
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.41
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.46
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.45
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.45
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.45
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.45
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.45
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.42
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.42
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.42
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.36
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.33
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.26
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.28
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.26
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rpsA 1833467 c.-75G>A upstream_gene_variant 0.17
rpsA 1833968 p.Gly143Trp missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834964 c.1428delA frameshift_variant 0.95
tlyA 1917919 c.-21C>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102030 p.Gln338Arg missense_variant 0.11
ndh 2102141 p.Gly301Asp missense_variant 0.17
ndh 2102261 c.781delG frameshift_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169622 p.Phe331Leu missense_variant 0.15
PPE35 2169625 p.Gly330Cys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518512 p.Gly133Val missense_variant 0.22
eis 2714471 c.861delT frameshift_variant 0.12
ahpC 2726611 p.Pro140His missense_variant 0.13
folC 2746249 c.1350C>A synonymous_variant 0.29
folC 2747068 c.530delT frameshift_variant 0.12
pepQ 2860540 c.-127_-123delGCATC upstream_gene_variant 0.11
ribD 2987027 c.189C>A synonymous_variant 0.15
Rv2752c 3067182 c.-991C>A upstream_gene_variant 0.15
thyX 3068100 c.-155C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087235 p.Arg139Leu missense_variant 0.12
ald 3087841 p.Lys341Ile missense_variant 0.11
fbiD 3338963 c.-155delC upstream_gene_variant 0.12
fbiD 3338995 c.-123G>A upstream_gene_variant 0.12
Rv3083 3448910 p.Leu136Pro missense_variant 0.18
Rv3083 3449307 c.804G>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475028 c.1026dupC frameshift_variant 0.18
fprA 3475363 c.1359dupT frameshift_variant 0.25
Rv3236c 3612505 p.His204Gln missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641059 c.519_520delGG frameshift_variant 0.12
alr 3841411 c.9delG frameshift_variant 0.15
rpoA 3877520 p.Trp330Arg missense_variant 0.15
clpC1 4038202 p.Ala835Ser missense_variant 0.18
clpC1 4039214 p.Phe497Leu missense_variant 0.29
clpC1 4040028 c.675_676delCG frameshift_variant 0.2
clpC1 4040187 c.517delC frameshift_variant 0.4
panD 4043992 p.Arg97Leu missense_variant 0.12
embC 4239848 c.-15G>A upstream_gene_variant 0.12
embC 4240307 p.Gly149Cys missense_variant 0.33
embC 4241231 p.Arg457Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.93
embA 4245243 p.Ala671Thr missense_variant 0.17
embA 4245603 p.Gly791Arg missense_variant 0.4
embB 4245710 c.-804G>A upstream_gene_variant 0.25
embA 4246303 p.Ser1024Asn missense_variant 0.12
embB 4247435 c.923delG frameshift_variant 0.11
embB 4249250 p.Ala913Thr missense_variant 0.22
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