TB-Profiler result

Run: SRR16295790
Summary

Run ID: SRR16295790

Sample name:

Date: 03-04-2023 17:02:19

Number of reads: 3488172

Percentage reads mapped: 51.66

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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 0.4 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 6192 p.Glu318Gly missense_variant 0.17
gyrA 7349 p.Glu16Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7580 c.279C>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8623 p.Arg441Gln missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490952 p.Trp57* stop_gained 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.64
mshA 576111 p.Ala255Gly missense_variant 0.29
mshA 576117 p.Ala257Val missense_variant 0.2
mshA 576755 p.Arg470Cys missense_variant 0.12
ccsA 620136 c.246C>A synonymous_variant 0.12
rpoB 760969 p.Ser388Leu missense_variant 0.12
rpoB 761599 p.Arg598His missense_variant 0.12
rpoB 761628 p.Gln608Lys missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764039 p.Ser224Arg missense_variant 0.13
rpoC 765987 p.Leu873Pro missense_variant 0.12
rpoC 766014 p.Gln882Arg missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775922 c.2559G>A synonymous_variant 0.18
mmpL5 776082 p.Ala800Val missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779203 p.Arg72Trp missense_variant 0.92
mmpL5 779379 c.-899C>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407152 c.189C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.21
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.39
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.39
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.41
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.39
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.41
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.39
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.39
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
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 1472598 n.753A>C non_coding_transcript_exon_variant 0.41
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.41
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.52
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.47
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.47
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.47
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.44
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.47
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.47
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.47
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.47
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.45
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.45
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.4
rrs 1472952 n.1108_1112delGTCTC non_coding_transcript_exon_variant 0.19
rrs 1472959 n.1114_1115insTGTTA non_coding_transcript_exon_variant 0.18
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.18
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.18
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.18
rrs 1472973 n.1129_1130delAT non_coding_transcript_exon_variant 0.17
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.17
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.19
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.19
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.19
rrs 1472990 n.1145A>C non_coding_transcript_exon_variant 0.19
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.18
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.18
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.18
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.25
rrl 1473811 n.154C>A non_coding_transcript_exon_variant 0.12
rrl 1474925 n.1268G>A non_coding_transcript_exon_variant 0.13
rrl 1476072 n.2415T>A non_coding_transcript_exon_variant 0.23
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.43
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.61
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.55
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.47
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.47
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.48
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.46
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.46
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.46
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.43
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.43
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.43
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.43
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.45
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.6
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.59
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.61
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.61
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.6
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.6
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.59
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.44
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.42
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.43
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.43
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.43
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.43
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.43
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.42
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.42
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.43
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.67
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.7
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.77
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.75
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75
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 1476481 n.2824T>C non_coding_transcript_exon_variant 0.82
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.74
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.71
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.69
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.65
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.66
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.67
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.64
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.64
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.62
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.64
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.6
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.58
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.58
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.56
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.56
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.51
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.4
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.3
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.12
inhA 1673496 c.-706G>T upstream_gene_variant 0.22
fabG1 1673711 p.Leu91Pro missense_variant 0.14
fabG1 1673969 p.Thr177Ile missense_variant 0.18
rpsA 1833641 p.Asn34Asp missense_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102276 p.Gly256Asp missense_variant 0.11
ndh 2102778 p.Val89Ile missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222837 p.Ala110Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288690 c.552C>T synonymous_variant 0.25
eis 2715467 c.-135A>G upstream_gene_variant 1.0
folC 2746250 p.Ala450Val missense_variant 0.2
folC 2746336 c.1263C>T synonymous_variant 0.13
folC 2747251 c.348C>T synonymous_variant 0.11
pepQ 2859866 p.Ala185Thr missense_variant 0.13
ribD 2987004 p.Asp56Asn missense_variant 0.11
Rv2752c 3065319 c.873C>T synonymous_variant 0.17
Rv2752c 3066324 c.-133G>T upstream_gene_variant 0.14
thyA 3073970 p.Ala168Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339213 c.96G>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474723 c.717C>A synonymous_variant 0.11
fprA 3474793 p.Gly263* stop_gained 0.11
Rv3236c 3612413 p.Ser235Leu missense_variant 0.17
Rv3236c 3612421 c.696G>A synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiA 3641224 p.Gly228Trp missense_variant 0.29
fbiA 3641287 p.Glu249* stop_gained 0.12
alr 3841120 p.Arg101Cys missense_variant 0.12
rpoA 3878010 c.498C>G synonymous_variant 0.11
rpoA 3878487 c.21C>A synonymous_variant 0.25
rpoA 3878567 c.-60C>G upstream_gene_variant 0.2
rpoA 3878569 c.-62C>G upstream_gene_variant 0.18
rpoA 3878609 c.-102T>A upstream_gene_variant 0.18
rpoA 3878639 c.-132C>G upstream_gene_variant 0.22
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
clpC1 4038208 p.Ala833Thr missense_variant 0.17
clpC1 4040127 p.Arg193His missense_variant 0.17
clpC1 4040249 p.Glu152Asp missense_variant 0.24
panD 4044469 c.-188G>A upstream_gene_variant 0.12
embC 4241433 p.Met524Lys missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242756 p.Ile965Asn missense_variant 0.16
embC 4242768 p.Arg969His missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244828 c.1596G>A synonymous_variant 0.11
embA 4244872 p.Gly547Asp missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246590 p.Thr26Met missense_variant 0.14
embB 4246762 c.249G>T synonymous_variant 0.12
embB 4247024 p.Pro171Ala missense_variant 0.32
aftB 4267187 c.1650T>A synonymous_variant 0.15
aftB 4267190 c.1647T>A synonymous_variant 0.15
aftB 4267196 p.Tyr547* stop_gained 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethA 4326866 p.Thr203Met missense_variant 0.15
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