TB-Profiler result

Run: SRR17406743
Summary

Run ID: SRR17406743

Sample name:

Date: 03-04-2023 17:58:50

Number of reads: 2574535

Percentage reads mapped: 89.35

Strain: lineage1.1.2

Drug-resistance: HR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_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 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
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
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407459 c.-119T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.15
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.16
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.16
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.16
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.16
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.16
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.15
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.15
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.16
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.16
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.17
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.17
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.12
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.12
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.11
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.11
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.11
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.11
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.11
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.11
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.12
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.12
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.3
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.33
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.42
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.47
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.47
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.43
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.44
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.43
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 1476302 n.2645G>A non_coding_transcript_exon_variant 0.43
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.43
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.44
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.44
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.57
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.57
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.58
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.51
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.52
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.46
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.45
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.3
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.28
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.28
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.28
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.29
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.29
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.29
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.29
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.28
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.22
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.22
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
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 2167983 p.Gly877Asp 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
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.97
Rv3236c 3612709 c.408G>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C 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