TB-Profiler result

Run: SRR3675273
Summary

Run ID: SRR3675273

Sample name:

Date: 04-04-2023 05:25:07

Number of reads: 810998

Percentage reads mapped: 80.31

Strain: lineage3

Drug-resistance: Sensitive

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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
lineage3 East-African-Indian CAS RD750 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
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 5094 c.-146G>T upstream_gene_variant 0.11
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 491124 c.342C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575660 p.Pro105Thr missense_variant 0.12
mshA 576278 p.Gly311* stop_gained 0.11
ccsA 619771 c.-120C>A upstream_gene_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760042 p.Gly79Val missense_variant 0.11
rpoB 761030 c.1224G>A synonymous_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762609 p.His935Tyr missense_variant 0.18
rpoC 762791 c.-579G>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764578 c.1209C>A synonymous_variant 0.2
rpoC 764660 p.Val431Met missense_variant 0.12
rpoC 764988 p.Gln540Leu missense_variant 0.13
rpoC 765752 p.Asp795Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775682 c.2799C>A synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778016 c.464delG frameshift_variant 0.18
mmpL5 778086 c.394delG frameshift_variant 0.22
mmpL5 778369 p.Gly38Trp missense_variant 0.14
mmpL5 778780 c.-300G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406670 p.Val224Ala missense_variant 0.11
embR 1417197 p.Gly51Arg missense_variant 0.17
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 0.2
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.2
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.22
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.2
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.13
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.13
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>A non_coding_transcript_exon_variant 0.24
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.29
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.29
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.35
rrs 1472560 n.715G>T non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.35
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.35
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.32
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.35
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.3
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.29
rrs 1472678 n.833T>C non_coding_transcript_exon_variant 0.2
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.2
rrs 1472681 n.838_843delTGGGAT non_coding_transcript_exon_variant 0.2
rrs 1472690 n.845C>G non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472726 n.881G>A non_coding_transcript_exon_variant 0.2
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.23
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.17
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.12
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.12
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.11
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.12
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.15
rrs 1473000 n.1155G>A non_coding_transcript_exon_variant 0.14
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.15
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.14
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.14
rrs 1473010 n.1165C>T non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.15
rrl 1473771 n.114T>A non_coding_transcript_exon_variant 0.12
rrl 1473851 n.194G>T non_coding_transcript_exon_variant 0.11
rrl 1474600 n.943C>G non_coding_transcript_exon_variant 0.12
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.11
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.2
rrl 1475715 n.2058G>A non_coding_transcript_exon_variant 0.2
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.2
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.22
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.22
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.22
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.22
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.22
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.23
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.23
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1475821 n.2166delA non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.36
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.58
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.61
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.53
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.56
rrl 1476518 n.2861G>A non_coding_transcript_exon_variant 0.53
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.59
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.59
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.59
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.59
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.62
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.59
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.56
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.47
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.43
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.33
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.2
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.2
fabG1 1673347 c.-93C>G upstream_gene_variant 0.14
inhA 1674453 c.252G>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154887 p.Ala409Ser missense_variant 0.17
katG 2155900 p.Ile71Thr missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168073 p.Pro847Gln missense_variant 0.14
PPE35 2169752 p.Phe287Leu missense_variant 0.12
PPE35 2169781 p.Gly278* stop_gained 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289027 p.Cys72Phe missense_variant 0.2
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289949 c.-708A>G upstream_gene_variant 0.22
pncA 2290034 c.-793C>A upstream_gene_variant 0.15
kasA 2518903 c.789C>A synonymous_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747273 p.Ser109* stop_gained 0.13
Rv2752c 3065736 p.Asp152Glu missense_variant 0.11
thyX 3068049 c.-104C>A upstream_gene_variant 0.17
thyX 3068058 c.-113G>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568655 p.Gln9Lys missense_variant 0.12
fbiA 3640882 p.Val114Leu missense_variant 0.2
alr 3841089 p.Ala111Asp missense_variant 0.17
rpoA 3877701 c.807G>T synonymous_variant 0.13
rpoA 3878699 c.-192C>A upstream_gene_variant 0.17
ddn 3986897 c.54C>A synonymous_variant 0.17
panD 4044266 p.Leu6Met missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242627 p.Ala922Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245374 c.2142G>T synonymous_variant 0.18
embA 4246070 c.2840delA frameshift_variant 0.13
embB 4246820 p.Pro103Ser missense_variant 0.12
embB 4247843 p.Val444Leu missense_variant 0.14
embB 4247884 c.1371C>A synonymous_variant 0.15
embB 4248523 c.2010A>G synonymous_variant 0.11
embB 4248860 p.Val783Ile missense_variant 0.13
aftB 4268162 p.Gln225His missense_variant 0.14
ubiA 4270012 c.-179G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0