TB-Profiler result

Run: SRR5007180
Summary

Run ID: SRR5007180

Sample name:

Date: 04-04-2023 07:52:02

Number of reads: 295578

Percentage reads mapped: 23.27

Strain:

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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 0.77 streptomycin
pncA 2288886 p.Trp119* stop_gained 0.5 pyrazinamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576567 p.Arg407Gln missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.2
rpoB 759711 c.-96G>A upstream_gene_variant 0.15
rpoB 759921 p.Arg39Cys missense_variant 0.12
rpoB 760814 c.1008C>T synonymous_variant 0.15
rpoB 761483 c.1677G>T synonymous_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765650 p.Gln761* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777009 p.Pro491Leu missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781788 c.230_232delACT disruptive_inframe_deletion 0.12
fbiC 1305435 c.2505G>A synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417371 c.-24A>G upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.29
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.13
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.57
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.61
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.62
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.71
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.71
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.72
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.72
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.65
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.68
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.6
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.46
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.7
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.69
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.67
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.54
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.78
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.78
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.78
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.58
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.35
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.6
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.55
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.75
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.66
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.78
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.71
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.7
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.23
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.19
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.14
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.15
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.17
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.14
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.13
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.13
rrl 1474869 n.1212G>C non_coding_transcript_exon_variant 0.12
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.13
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.18
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.18
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.22
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.24
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.16
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.23
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.24
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.27
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.25
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.24
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.2
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.14
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.14
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.21
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.41
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.44
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.44
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.4
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.4
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.42
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.39
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.42
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.42
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.42
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.42
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.42
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.43
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.66
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.59
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.67
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.75
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.82
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.71
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.82
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.81
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.72
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.75
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.74
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.74
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.71
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.69
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.72
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.73
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.74
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.73
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.79
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.77
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.84
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.85
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.85
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.84
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.89
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.89
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.88
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.82
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.63
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.54
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.42
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.48
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.47
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.33
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.21
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.13
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.13
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.14
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918399 p.Asp154Tyr missense_variant 0.29
tlyA 1918513 p.Val192Ile missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169178 p.Ala479Thr missense_variant 0.2
PPE35 2170312 p.Arg101Trp missense_variant 0.4
Rv1979c 2222069 p.Ala366Thr missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.3
kasA 2518161 p.Val16Gly missense_variant 0.25
pepQ 2860367 p.Gly18Arg missense_variant 0.2
ald 3086747 c.-73A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087483 p.Ala222Pro missense_variant 0.17
fprA 3473853 c.-154C>T upstream_gene_variant 0.22
fprA 3473928 c.-79T>C upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568547 c.131_132dupTG frameshift_variant 0.18
Rv3236c 3613142 c.-26A>G upstream_gene_variant 0.33
Rv3236c 3613167 c.-51C>A upstream_gene_variant 0.4
clpC1 4039484 c.1221T>G synonymous_variant 0.33
clpC1 4040162 c.543G>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246509 c.-5C>T upstream_gene_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269864 c.-31C>G upstream_gene_variant 0.5
ethR 4327105 c.-444G>A upstream_gene_variant 0.17
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