TB-Profiler result

Run: SRR6855768
Summary

Run ID: SRR6855768

Sample name:

Date: 04-04-2023 17:44:58

Number of reads: 381184

Percentage reads mapped: 89.46

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
tlyA 1918388 c.451delG frameshift_variant 0.18 capreomycin
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 5520 p.Pro94Leu missense_variant 0.94
gyrB 5687 p.Tyr150His missense_variant 0.1
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8374 c.1075delG frameshift_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490618 c.-165T>C upstream_gene_variant 0.11
fgd1 491168 p.Phe129Ser missense_variant 0.1
fgd1 491584 c.803delT frameshift_variant 0.11
mshA 575690 p.Gly115Arg missense_variant 0.12
rpoB 762183 c.2380delG frameshift_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766192 c.2824delC frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776372 c.2109C>G synonymous_variant 0.12
mmpL5 776515 p.His656Asp missense_variant 0.18
mmpL5 777258 c.1222dupC frameshift_variant 0.1
mmpL5 777721 p.Arg254Trp missense_variant 0.12
mmpL5 778912 c.-432G>T upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781515 c.-45G>A upstream_gene_variant 0.12
rplC 800843 p.Gly12Asp missense_variant 0.12
fbiC 1303034 p.Asp35Val missense_variant 0.14
Rv1258c 1406802 c.538delG frameshift_variant 0.14
Rv1258c 1407157 p.Ala62Thr missense_variant 0.12
embR 1416258 p.Asn364Asp missense_variant 0.11
atpE 1461092 c.49delA frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.1
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.1
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.1
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.11
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.12
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.11
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.1
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.11
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.12
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.12
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.11
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.11
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.11
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.11
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.13
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrl 1475404 n.1747A>G non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.1
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.19
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.19
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.19
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.2
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.28
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.3
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.19
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.2
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.2
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.2
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.2
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.2
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 0.19
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.24
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.24
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.24
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.25
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.14
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.13
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.13
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.14
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.13
fabG1 1673526 c.87_88insT frameshift_variant 0.2
inhA 1673535 c.-667A>C upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102645 c.395_397dupCCG conservative_inframe_insertion 0.29
PPE35 2169075 p.Ile513Thr missense_variant 0.12
Rv1979c 2222493 c.672C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746523 c.1075delG frameshift_variant 0.14
folC 2746752 p.Gly283Cys missense_variant 0.17
folC 2747282 p.Glu106Gly missense_variant 0.11
pepQ 2860075 p.Glu115Gly missense_variant 0.2
ribD 2987548 p.Arg237Gln missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474823 p.Thr273Ala missense_variant 0.14
Rv3236c 3612013 c.1104A>T synonymous_variant 0.13
Rv3236c 3612307 p.Phe270Leu missense_variant 0.18
fbiB 3641936 c.402C>T synonymous_variant 0.12
fbiB 3641960 c.426C>A synonymous_variant 0.13
fbiB 3642028 p.Val165Asp missense_variant 0.22
ddn 3987090 p.Glu83Lys missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038494 c.2211G>A synonymous_variant 0.12
clpC1 4038732 p.Lys658Arg missense_variant 0.12
clpC1 4039095 c.1609delG frameshift_variant 0.12
clpC1 4039793 c.912C>T synonymous_variant 0.12
clpC1 4040095 c.608_609dupTG frameshift_variant 0.15
panD 4044186 c.95dupT frameshift_variant 0.25
embC 4241276 c.1414C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245968 c.2738dupC frameshift_variant 0.15
embB 4248378 p.Ser622* stop_gained 0.14
embB 4249609 c.3098delA frameshift_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408092 c.111A>C synonymous_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408162 p.Pro14Leu missense_variant 0.12