TB-Profiler result

Run: SRR16295798
Summary

Run ID: SRR16295798

Sample name:

Date: 03-04-2023 17:08:55

Number of reads: 5574678

Percentage reads mapped: 73.06

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 0.28 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 6237 p.Lys333Arg missense_variant 0.13
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 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.51
mshA 576258 p.Ser304Ile missense_variant 0.14
ccsA 620292 c.402C>T synonymous_variant 0.12
rpoC 762932 c.-438G>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763845 p.Arg159His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778501 c.-21C>A upstream_gene_variant 0.11
mmpR5 779263 c.275dupA frameshift_variant&stop_gained 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.12
fbiC 1303155 c.225G>A synonymous_variant 0.16
fbiC 1303980 c.1050G>T synonymous_variant 0.13
fbiC 1304101 p.Arg391Trp missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407184 c.157C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472287 n.442C>A non_coding_transcript_exon_variant 0.14
rrs 1472451 n.606C>T non_coding_transcript_exon_variant 0.12
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.22
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.21
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.21
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.26
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.28
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.28
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.28
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.27
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.24
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.26
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.26
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.26
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.26
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.29
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.29
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.28
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.21
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.19
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.19
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.2
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.18
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.18
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.18
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.18
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.18
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.35
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.36
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.43
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.42
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.45
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.44
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 0.43
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 0.42
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 0.44
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.44
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.45
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.63
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.66
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.7
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.72
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.7
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.63
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.63
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.65
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.66
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.59
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.58
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.53
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.55
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.53
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.54
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.53
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.54
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.55
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.55
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.55
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.54
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.45
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.46
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.45
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.44
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.41
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.29
rrl 1476602 n.2945G>A non_coding_transcript_exon_variant 0.22
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.15
fabG1 1673279 c.-161G>A upstream_gene_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154237 c.1875G>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154981 p.Met377Ile missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714223 c.1110C>G synonymous_variant 0.11
eis 2715467 c.-135A>G upstream_gene_variant 1.0
folC 2747589 p.Thr4Ser missense_variant 0.12
pepQ 2860481 c.-63C>A upstream_gene_variant 0.11
Rv2752c 3064734 c.1458G>A synonymous_variant 0.12
Rv2752c 3065998 p.Arg65His missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087085 p.Gln89Arg missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612505 c.612T>C synonymous_variant 0.12
Rv3236c 3612774 c.342delC frameshift_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiA 3641333 p.Gly264Ala missense_variant 0.16
fbiA 3641340 p.Asp266Glu missense_variant 0.17
rpoA 3878567 c.-60C>G upstream_gene_variant 0.22
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17
rpoA 3878639 c.-132C>G upstream_gene_variant 0.15
clpC1 4038183 p.Gly841Ala missense_variant 0.11
clpC1 4039570 p.Met379Leu missense_variant 0.24
embC 4241921 p.Gly687Trp missense_variant 0.12
embC 4241925 p.Arg688Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243570 p.Thr113Met missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4248956 p.Trp815Arg missense_variant 0.14
embB 4249324 c.2811A>G synonymous_variant 0.13
aftB 4267478 c.1359G>A synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
ethR 4326928 c.-621G>T upstream_gene_variant 0.11
ethA 4326935 p.Val180Glu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338609 c.-88T>C upstream_gene_variant 0.11
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0