TB-Profiler result

Run: SRR2101572
Summary

Run ID: SRR2101572

Sample name:

Date: 03-04-2023 23:47:49

Number of reads: 416189

Percentage reads mapped: 97.52

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA RD239 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
rpoB 761083 c.1278_1286delCACCAGCCA disruptive_inframe_deletion 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.3 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7335 p.Leu12Phe missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9207 p.Lys636Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620537 p.Val216Gly missense_variant 0.14
ccsA 620659 p.Arg257Cys missense_variant 1.0
rpoB 760384 p.Leu193Pro missense_variant 0.29
rpoC 762713 c.-657G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrs 1472236 n.391C>T non_coding_transcript_exon_variant 0.11
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.16
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.17
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.32
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.39
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.39
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.34
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.38
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.34
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.34
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.37
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.37
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.28
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.34
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.37
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.34
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.34
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.31
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.31
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.18
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrl 1473537 n.-121C>G upstream_gene_variant 0.1
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.21
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.3
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.28
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.26
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.26
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.26
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.25
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.3
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.3
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.24
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.23
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.27
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.23
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.23
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.27
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.3
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.3
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
rrl 1476515 n.2858C>A non_coding_transcript_exon_variant 0.14
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15
fabG1 1674168 p.Met243Ile missense_variant 0.11
inhA 1674651 p.Asp150Glu missense_variant 0.12
inhA 1674835 c.637_638delGC frameshift_variant 0.15
inhA 1674962 p.Thr254Lys missense_variant 0.15
rpsA 1834583 p.Val348Ile missense_variant 0.11
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518724 p.Ala204Ser missense_variant 0.22
kasA 2518757 p.Ala215Ser missense_variant 0.22
kasA 2519259 p.Leu382His missense_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3065159 p.Glu345* stop_gained 0.15
Rv2752c 3065179 p.Ser338* stop_gained 0.14
thyX 3068115 c.-170C>T upstream_gene_variant 1.0
thyA 3074034 c.438T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338961 c.-157G>T upstream_gene_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474469 p.Asn155Asp missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612504 p.His205Asn missense_variant 0.15
Rv3236c 3612873 p.Phe82Leu missense_variant 0.2
Rv3236c 3612992 p.Ser42Leu missense_variant 0.22
fbiA 3640417 c.-126C>T upstream_gene_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4266955 c.1882T>A stop_lost&splice_region_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0