TB-Profiler result

Run: SRR13861329
Summary

Run ID: SRR13861329

Sample name:

Date: 03-04-2023 09:29:07

Number of reads: 451351

Percentage reads mapped: 45.18

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 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
gyrA 8393 c.1092T>C synonymous_variant 0.13
gyrA 8399 c.1098T>C synonymous_variant 0.14
gyrA 8442 c.1141C>T synonymous_variant 0.12
gyrA 8453 c.1152A>C synonymous_variant 0.12
gyrA 8462 c.1161A>G synonymous_variant 0.12
gyrA 8471 c.1170T>C synonymous_variant 0.12
gyrA 8480 c.1179C>T synonymous_variant 0.13
gyrA 8486 c.1185T>C synonymous_variant 0.13
gyrA 8489 c.1188A>G synonymous_variant 0.13
gyrA 8498 c.1197C>T synonymous_variant 0.18
gyrA 8504 c.1203G>C synonymous_variant 0.19
gyrA 8516 c.1215T>C synonymous_variant 0.19
gyrA 8519 c.1218A>C synonymous_variant 0.12
gyrA 9774 p.Asp825Asn missense_variant 0.18
ccsA 620144 c.255dupT frameshift_variant 1.0
rpoB 760191 p.Val129Phe missense_variant 1.0
rpoB 760311 p.Val169Leu missense_variant 1.0
rpoB 761222 c.1416G>C synonymous_variant 0.12
rpoB 761249 c.1443A>G synonymous_variant 0.12
rpoB 761261 c.1455G>T synonymous_variant 0.12
rpoB 761327 c.1521A>G synonymous_variant 0.12
rpoB 761570 c.1764T>C synonymous_variant 0.14
rpoB 761573 c.1767C>G synonymous_variant 0.14
rpoB 761579 c.1773G>C synonymous_variant 0.13
rpoB 761606 c.1800C>G synonymous_variant 0.14
rpoB 761612 c.1806G>C synonymous_variant 0.17
rpoB 761615 c.1809A>C synonymous_variant 0.13
rpoB 761648 c.1842T>C synonymous_variant 0.14
rpoB 761657 c.1851C>G synonymous_variant 0.14
rpoB 761675 c.1869G>C synonymous_variant 0.18
rpoB 761687 c.1881C>T synonymous_variant 0.19
rpoB 761690 c.1884G>C synonymous_variant 0.15
rpoB 761732 c.1926C>G synonymous_variant 0.15
rpoB 761735 c.1929C>G synonymous_variant 0.14
rpoB 761747 c.1941G>C synonymous_variant 0.16
rpoB 761750 c.1944G>C synonymous_variant 0.15
rpoB 761765 c.1959T>C synonymous_variant 0.18
rpoB 761772 p.His656Ala missense_variant 0.18
rpoB 761778 p.Asn658Asp missense_variant 0.19
rpoB 761791 p.Arg662His missense_variant 0.12
rpoB 761834 c.2028T>C synonymous_variant 0.16
rpoB 761847 p.Cys681Ser missense_variant 0.11
rpoB 761885 c.2079T>C synonymous_variant 0.12
rpoB 761948 c.2142G>C synonymous_variant 0.12
rpoB 761954 c.2148C>G synonymous_variant 0.13
rpoB 762805 p.Gly1000Asp missense_variant 1.0
rpoB 762963 p.Gly1053Arg missense_variant 0.94
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.12
rpoC 763570 c.201G>C synonymous_variant 0.13
rpoC 763633 c.264T>C synonymous_variant 0.2
rpoC 763636 c.267T>C synonymous_variant 0.2
rpoC 763642 c.273G>C synonymous_variant 0.25
rpoC 763658 c.289_291delCTTinsTTG synonymous_variant 0.17
rpoC 763662 p.Ala98Asp missense_variant 0.82
rpoC 763675 c.306C>G synonymous_variant 0.2
rpoC 763696 c.327T>C synonymous_variant 0.27
rpoC 763702 c.333C>G synonymous_variant 0.27
rpoC 763708 c.339G>A synonymous_variant 0.27
rpoC 763709 c.340C>T synonymous_variant 0.27
rpoC 763714 c.345G>C synonymous_variant 0.27
rpoC 763717 c.348T>C synonymous_variant 0.27
rpoC 763723 c.354G>C synonymous_variant 0.27
rpoC 763732 c.363C>G synonymous_variant 0.27
rpoC 763735 c.366G>C synonymous_variant 0.33
rpoC 763744 c.375G>C synonymous_variant 0.31
rpoC 763765 c.396T>C synonymous_variant 0.23
rpoC 763768 c.399C>G synonymous_variant 0.23
rpoC 763780 c.411C>G synonymous_variant 0.2
rpoC 763783 c.414G>C synonymous_variant 0.2
rpoC 763807 c.438T>C synonymous_variant 0.13
rpoC 763819 c.450G>C synonymous_variant 0.13
mmpL5 776041 p.Ala814Thr missense_variant 0.92
mmpL5 776070 c.2410delA frameshift_variant 1.0
mmpL5 777800 c.681C>T synonymous_variant 1.0
rplC 800865 c.57A>G synonymous_variant 0.12
rplC 800867 p.Ser20Asn missense_variant 0.12
fbiC 1304996 p.Leu689Ser missense_variant 1.0
Rv1258c 1407148 p.Ala65Ser missense_variant 1.0
embR 1416842 p.Asp169Gly missense_variant 1.0
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.12
rrs 1472031 n.186G>A non_coding_transcript_exon_variant 0.12
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.13
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.12
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.12
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.12
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.29
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.47
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.39
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.53
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.53
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.61
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.54
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.53
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.57
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.59
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.59
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.53
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.53
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.54
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.54
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.51
rrs 1472230 n.385C>T non_coding_transcript_exon_variant 0.24
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.53
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.53
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.51
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.45
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.41
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.3
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.26
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.12
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.12
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.3
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.3
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.28
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.26
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.26
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.26
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.24
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.24
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.26
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.38
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.41
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.47
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.46
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.44
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.43
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.43
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.43
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.42
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.22
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.18
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.17
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.17
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.15
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.15
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.15
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.15
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.14
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.14
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.15
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.18
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.17
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.34
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.56
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.55
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.57
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.59
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.59
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.53
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.53
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.55
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.55
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.54
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.55
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.56
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 0.59
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.74
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.77
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.84
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.83
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.66
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.83
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.83
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.85
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.77
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.7
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.62
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.62
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.65
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.65
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.65
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.65
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.65
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.65
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.67
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.69
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.59
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.59
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.59
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.62
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.19
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.13
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.13
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.12
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.12
inhA 1674940 c.739_740insG frameshift_variant 1.0
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.15
rpsA 1834102 c.561T>C synonymous_variant 0.14
rpsA 1834411 c.870T>C synonymous_variant 0.12
rpsA 1834423 c.882G>C synonymous_variant 0.12
rpsA 1834528 c.987T>C synonymous_variant 0.17
rpsA 1834546 c.1005T>C synonymous_variant 0.17
rpsA 1834555 c.1014T>C synonymous_variant 0.16
rpsA 1834624 c.1083G>C synonymous_variant 0.12
rpsA 1834639 c.1098T>C synonymous_variant 0.13
ndh 2102590 c.453A>C synonymous_variant 0.17
ndh 2102694 p.Val117Ile missense_variant 1.0
katG 2155865 p.Val83Met missense_variant 1.0
PPE35 2168123 c.2489dupG frameshift_variant 1.0
PPE35 2170268 c.345C>A synonymous_variant 1.0
kasA 2518311 p.Asp66Gly missense_variant 1.0
kasA 2518642 c.528A>G synonymous_variant 0.12
eis 2714666 p.Tyr223Asp missense_variant 1.0
ahpC 2726589 p.Arg133Ser missense_variant 1.0
pepQ 2859467 p.Ala318Thr missense_variant 0.14
Rv2752c 3065979 c.213T>C synonymous_variant 0.2
Rv2752c 3065993 p.Val67Ile missense_variant 0.25
Rv2752c 3065994 c.198T>C synonymous_variant 0.23
Rv2752c 3065997 c.195C>G synonymous_variant 0.23
Rv2752c 3066002 p.Met64Leu missense_variant 0.21
Rv2752c 3066024 c.168T>C synonymous_variant 0.25
Rv2752c 3066040 p.Gly51Thr missense_variant 0.15
Rv2752c 3066042 c.150T>C synonymous_variant 0.15
Rv2752c 3066050 p.Leu48Met missense_variant 0.15
Rv2752c 3066054 c.138T>G synonymous_variant 0.15
Rv2752c 3066075 c.117A>G synonymous_variant 0.17
Rv2752c 3066087 c.105A>G synonymous_variant 0.14
Rv2752c 3066289 c.-98T>G upstream_gene_variant 1.0
thyA 3074418 p.Lys18Asn missense_variant 1.0
ald 3087163 c.344_345insC frameshift_variant 1.0
Rv3236c 3612049 c.1068G>C synonymous_variant 1.0
Rv3236c 3612400 c.717G>A synonymous_variant 1.0
fbiB 3642445 p.Ala304Gly missense_variant 1.0
clpC1 4038941 c.1764G>C synonymous_variant 0.92
clpC1 4039274 c.1431G>C synonymous_variant 0.18
clpC1 4039286 c.1419T>C synonymous_variant 0.18
clpC1 4040104 p.Met201Leu missense_variant 0.92
embC 4241480 c.1618T>C synonymous_variant 1.0
embB 4249483 c.2970C>G synonymous_variant 1.0
aftB 4268164 c.672_673insA frameshift_variant 1.0
ethA 4327641 c.-168G>A upstream_gene_variant 1.0