TB-Profiler result

Run: SRR14088362
Summary

Run ID: SRR14088362

Sample name:

Date: 03-04-2023 09:45:49

Number of reads: 1648420

Percentage reads mapped: 96.4

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
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
ccsA 620128 p.Gly80Arg missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764541 p.Val391Gly missense_variant 0.13
rpoC 764543 p.Thr392Asp missense_variant 0.13
rpoC 765075 p.Ala569Glu missense_variant 0.11
rpoC 766941 p.Arg1191His missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775768 p.Gln905Lys missense_variant 0.13
mmpL5 775910 c.2571G>A synonymous_variant 0.12
mmpL5 775915 p.Ala856Ser missense_variant 0.14
mmpL5 775927 c.2554C>T synonymous_variant 0.17
mmpL5 775931 c.2550C>T synonymous_variant 0.17
mmpL5 775957 p.Ile842Leu missense_variant 0.13
mmpL5 775961 c.2520C>G synonymous_variant 0.13
mmpL5 775966 p.Ala839Ser missense_variant 0.15
mmpL5 775981 p.Leu834Met missense_variant 0.15
mmpL5 775987 p.His832Tyr missense_variant 0.17
mmpL5 775990 c.2491C>T synonymous_variant 0.15
mmpL5 776052 p.Leu810Ser missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776589 p.Met631Thr missense_variant 0.11
mmpL5 778194 p.Glu96Val missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406555 p.Trp262* stop_gained 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.11
rrl 1476611 n.2954T>C non_coding_transcript_exon_variant 0.12
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.11
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.11
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.12
inhA 1674333 c.132G>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918553 p.Ala205Glu missense_variant 0.2
tlyA 1918558 p.Ser207Ala missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155834 p.Ala93Val missense_variant 0.12
katG 2156047 p.Val22Ala missense_variant 0.13
PPE35 2167745 p.Thr956Arg missense_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.35
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170066 p.Ala183Thr missense_variant 0.25
PPE35 2170370 p.Thr81Ala missense_variant 0.13
PPE35 2170377 p.Ala79Val missense_variant 0.15
PPE35 2170381 p.Ala78Ser missense_variant 0.15
PPE35 2170382 p.Ala77Gly missense_variant 0.15
PPE35 2170387 c.226C>T synonymous_variant 0.15
PPE35 2170406 c.207A>G synonymous_variant 0.15
PPE35 2170415 c.198A>C synonymous_variant 0.18
PPE35 2170454 c.159C>G synonymous_variant 0.15
PPE35 2170457 c.156G>C synonymous_variant 0.15
PPE35 2170460 c.153G>A synonymous_variant 0.14
PPE35 2170465 p.Ala50Ser missense_variant 0.12
PPE35 2170472 c.141G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288706 p.Ser179Asn missense_variant 0.14
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714666 p.Tyr223His missense_variant 0.11
eis 2714672 p.Asp221Asn missense_variant 0.12
eis 2714754 c.579G>A synonymous_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.2
folC 2747627 c.-29C>T upstream_gene_variant 0.22
pepQ 2859517 p.Gln301Arg missense_variant 0.14
pepQ 2859634 p.Gln262Arg missense_variant 0.14
ribD 2987306 c.468C>A synonymous_variant 0.18
Rv2752c 3064963 p.Ala410Asp missense_variant 0.11
Rv2752c 3064991 c.1201C>A synonymous_variant 0.12
Rv2752c 3065426 p.Gly256Cys missense_variant 0.12
Rv2752c 3065507 p.Ala229Ser missense_variant 0.12
Rv2752c 3066021 c.171C>G synonymous_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.12
thyX 3067439 p.Gln169His missense_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087391 p.Gly191Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475028 p.Ile341Asn missense_variant 0.15
fbiB 3641787 p.Val85Met missense_variant 0.12
fbiB 3642877 p.Lys448Arg missense_variant 0.95
alr 3841612 c.-193_-192insC upstream_gene_variant 0.2
clpC1 4039691 c.1014G>C synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.14
embC 4240661 p.Trp267Arg missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.32
embB 4246555 c.42G>C synonymous_variant 0.31
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4248628 c.2115C>A synonymous_variant 0.17
embB 4248725 p.Ser738Pro missense_variant 0.15
aftB 4267990 p.Ala283Thr missense_variant 0.17
aftB 4267993 p.Thr282Ser missense_variant 0.17
ubiA 4269140 p.Cys232Arg missense_variant 0.17
ethR 4326868 c.-681G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0