Run ID: SRR4036025
Sample name:
Date: 04-04-2023 07:27:10
Number of reads: 1151622
Percentage reads mapped: 99.47
Strain: lineage3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761095 | p.Leu430Pro | missense_variant | 0.11 | rifampicin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin |
ahpC | 2726142 | c.-51G>T | upstream_gene_variant | 0.14 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5590 | c.351T>A | synonymous_variant | 0.17 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8056 | p.Arg252Leu | missense_variant | 1.0 |
gyrA | 8875 | p.Tyr525Cys | missense_variant | 0.11 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9400 | p.Val700Ala | missense_variant | 0.25 |
gyrA | 9477 | p.Ala726Thr | missense_variant | 0.33 |
gyrA | 9708 | c.2407T>C | synonymous_variant | 0.12 |
gyrA | 9792 | p.Asn831Tyr | missense_variant | 0.17 |
fgd1 | 490701 | c.-82A>G | upstream_gene_variant | 0.12 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575264 | c.-84C>A | upstream_gene_variant | 0.15 |
mshA | 575285 | c.-63G>C | upstream_gene_variant | 0.12 |
mshA | 575397 | p.Arg17His | missense_variant | 0.18 |
mshA | 575678 | p.Asn111Asp | missense_variant | 0.12 |
mshA | 575799 | p.Val151Ala | missense_variant | 0.11 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 761191 | p.Ala462Gly | missense_variant | 0.12 |
rpoB | 761401 | p.Arg532His | missense_variant | 0.14 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763115 | c.-255T>C | upstream_gene_variant | 0.11 |
rpoC | 764745 | p.Arg459Gln | missense_variant | 0.15 |
rpoC | 764778 | p.Lys470Thr | missense_variant | 0.14 |
rpoC | 764834 | p.Glu489Lys | missense_variant | 0.14 |
rpoC | 764842 | p.Ile491Met | missense_variant | 0.14 |
rpoC | 764918 | p.Val517Leu | missense_variant | 0.17 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776271 | p.Lys737Met | missense_variant | 0.17 |
mmpL5 | 777036 | p.Gln482Arg | missense_variant | 0.17 |
mmpL5 | 777145 | p.Glu446Lys | missense_variant | 0.2 |
mmpL5 | 777226 | p.Asn419Asp | missense_variant | 0.2 |
rpsL | 781392 | c.-168C>T | upstream_gene_variant | 0.13 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781781 | c.222G>A | synonymous_variant | 0.15 |
rpsL | 781784 | p.Gln75His | missense_variant | 0.13 |
rplC | 800896 | p.Lys30Glu | missense_variant | 0.12 |
fbiC | 1304365 | p.Gln479* | stop_gained | 0.17 |
fbiC | 1304411 | p.Asp494Gly | missense_variant | 0.11 |
fbiC | 1304431 | p.Ser501Pro | missense_variant | 0.1 |
fbiC | 1304783 | p.Val618Asp | missense_variant | 0.12 |
fbiC | 1304868 | c.1938G>A | synonymous_variant | 0.15 |
Rv1258c | 1407339 | c.2T>A | start_lost | 0.14 |
embR | 1416224 | p.Glu375Ala | missense_variant | 0.1 |
embR | 1416790 | c.558G>A | synonymous_variant | 0.17 |
embR | 1416927 | p.Ala141Thr | missense_variant | 0.2 |
embR | 1417077 | p.Arg91Trp | missense_variant | 0.18 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472117 | n.272A>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1473909 | n.252G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475901 | n.2244C>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476708 | n.3051C>A | non_coding_transcript_exon_variant | 0.15 |
inhA | 1674605 | p.Leu135Pro | missense_variant | 0.11 |
rpsA | 1833373 | c.-169G>A | upstream_gene_variant | 0.17 |
rpsA | 1833426 | c.-116T>C | upstream_gene_variant | 0.17 |
rpsA | 1834139 | p.Ser200Cys | missense_variant | 0.13 |
rpsA | 1834264 | c.723G>A | synonymous_variant | 0.18 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102414 | p.Arg210Gln | missense_variant | 0.14 |
ndh | 2102421 | c.621dupC | frameshift_variant | 0.14 |
ndh | 2102471 | p.Glu191Ala | missense_variant | 0.15 |
ndh | 2102489 | p.Met185Lys | missense_variant | 0.17 |
ndh | 2102502 | p.Thr181Ala | missense_variant | 0.13 |
katG | 2154007 | p.Ser702Leu | missense_variant | 0.2 |
katG | 2154134 | p.Asn660Asp | missense_variant | 0.14 |
katG | 2154339 | c.1773A>G | synonymous_variant | 0.14 |
katG | 2154368 | p.Glu582Lys | missense_variant | 0.15 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2154937 | p.Arg392Gln | missense_variant | 0.15 |
katG | 2155056 | c.1056A>G | synonymous_variant | 0.2 |
katG | 2156134 | c.-23C>A | upstream_gene_variant | 0.12 |
katG | 2156440 | c.-329A>G | upstream_gene_variant | 0.12 |
PPE35 | 2167881 | p.Asn911Ser | missense_variant | 0.13 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168034 | p.Thr860Ile | missense_variant | 0.12 |
PPE35 | 2168143 | p.Phe824Val | missense_variant | 0.15 |
PPE35 | 2168168 | p.Met815Ile | missense_variant | 0.14 |
PPE35 | 2168176 | p.Gln813* | stop_gained | 0.13 |
PPE35 | 2168353 | p.Ile754Val | missense_variant | 0.11 |
PPE35 | 2168410 | p.Thr735Ala | missense_variant | 0.11 |
PPE35 | 2169459 | p.Gly385Asp | missense_variant | 0.13 |
PPE35 | 2170254 | p.Leu120Pro | missense_variant | 0.11 |
Rv1979c | 2221750 | p.Arg472Leu | missense_variant | 0.17 |
Rv1979c | 2222625 | c.540C>T | synonymous_variant | 0.25 |
Rv1979c | 2223025 | p.Ala47Val | missense_variant | 0.15 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv1979c | 2223333 | c.-169G>C | upstream_gene_variant | 0.14 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
pncA | 2289845 | c.-604G>A | upstream_gene_variant | 0.14 |
pncA | 2290018 | c.-777C>T | upstream_gene_variant | 0.2 |
kasA | 2518228 | c.114C>G | synonymous_variant | 0.13 |
kasA | 2519048 | p.Gly312Ser | missense_variant | 0.13 |
eis | 2714419 | p.Leu305His | missense_variant | 0.33 |
eis | 2714707 | p.Gly209Asp | missense_variant | 0.14 |
eis | 2714712 | c.621G>C | synonymous_variant | 0.14 |
eis | 2715131 | p.Arg68Trp | missense_variant | 0.14 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
folC | 2747692 | c.-94A>G | upstream_gene_variant | 0.14 |
pepQ | 2859488 | p.Thr311Ala | missense_variant | 0.12 |
pepQ | 2859775 | p.Gly215Asp | missense_variant | 0.15 |
ribD | 2986681 | c.-158A>T | upstream_gene_variant | 0.13 |
ribD | 2986693 | c.-146C>T | upstream_gene_variant | 0.13 |
ribD | 2986695 | c.-144A>G | upstream_gene_variant | 0.14 |
Rv2752c | 3064775 | p.Val473Ile | missense_variant | 0.13 |
Rv2752c | 3065379 | c.813C>T | synonymous_variant | 0.2 |
Rv2752c | 3067025 | c.-834G>C | upstream_gene_variant | 0.17 |
Rv2752c | 3067128 | c.-938delG | upstream_gene_variant | 0.13 |
thyA | 3074424 | c.48G>T | synonymous_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087187 | p.Ala123Val | missense_variant | 0.12 |
fbiD | 3338967 | c.-151C>T | upstream_gene_variant | 0.13 |
fbiD | 3339350 | p.Asp78Gly | missense_variant | 0.11 |
Rv3083 | 3448730 | p.Ala76Val | missense_variant | 0.13 |
Rv3083 | 3449942 | p.Asp480Gly | missense_variant | 0.12 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474465 | p.Ile153Met | missense_variant | 0.11 |
fprA | 3474663 | c.661delG | frameshift_variant | 0.22 |
whiB7 | 3568692 | c.-14delA | upstream_gene_variant | 0.14 |
whiB7 | 3568705 | c.-26A>G | upstream_gene_variant | 0.12 |
Rv3236c | 3612561 | p.Thr186Ser | missense_variant | 0.15 |
Rv3236c | 3612732 | c.384delC | frameshift_variant | 0.13 |
fbiA | 3640973 | p.Pro144Arg | missense_variant | 0.12 |
fbiA | 3641525 | p.Gly328Glu | missense_variant | 0.12 |
fbiB | 3641957 | c.423C>G | synonymous_variant | 0.15 |
fbiB | 3642489 | p.Ser319Pro | missense_variant | 0.17 |
alr | 3840825 | p.Tyr199Cys | missense_variant | 0.1 |
rpoA | 3877513 | p.Thr332Ile | missense_variant | 0.13 |
rpoA | 3878324 | p.Glu62Lys | missense_variant | 0.2 |
rpoA | 3878378 | p.Ser44Thr | missense_variant | 0.13 |
clpC1 | 4038494 | c.2211G>C | synonymous_variant | 0.13 |
clpC1 | 4039860 | p.Ile282Asn | missense_variant | 0.12 |
clpC1 | 4040073 | p.Asn211Ser | missense_variant | 0.12 |
embC | 4239734 | c.-129C>A | upstream_gene_variant | 0.22 |
embC | 4240702 | c.840G>A | synonymous_variant | 0.13 |
embC | 4241997 | p.Thr712Met | missense_variant | 0.12 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242310 | c.-923C>A | upstream_gene_variant | 0.18 |
embA | 4242316 | c.-917C>T | upstream_gene_variant | 0.29 |
embC | 4242320 | p.Pro820Ala | missense_variant | 0.25 |
embA | 4242586 | c.-647C>A | upstream_gene_variant | 0.33 |
embC | 4242606 | p.Met915Lys | missense_variant | 0.33 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242687 | p.Gln942Arg | missense_variant | 0.18 |
embA | 4242877 | c.-356G>A | upstream_gene_variant | 0.18 |
embC | 4242920 | p.Ala1020Thr | missense_variant | 0.14 |
embC | 4242933 | p.Val1024Ala | missense_variant | 0.14 |
embC | 4242951 | p.Gly1030Val | missense_variant | 0.14 |
embC | 4242963 | p.Gly1034Asp | missense_variant | 0.17 |
embC | 4242999 | p.Ala1046Val | missense_variant | 0.25 |
embA | 4245337 | p.Val702Gly | missense_variant | 0.12 |
embA | 4246056 | p.Val942Ile | missense_variant | 0.13 |
embB | 4246999 | c.486C>G | synonymous_variant | 0.22 |
embB | 4247284 | c.771G>A | synonymous_variant | 0.14 |
embB | 4247485 | c.972C>T | synonymous_variant | 0.14 |
embB | 4247498 | p.Pro329Ser | missense_variant | 0.15 |
embB | 4248638 | p.Ile709Phe | missense_variant | 0.25 |
aftB | 4267013 | c.1824T>C | synonymous_variant | 0.18 |
aftB | 4267472 | c.1364delG | frameshift_variant | 0.15 |
aftB | 4268113 | p.Ala242Pro | missense_variant | 0.14 |
aftB | 4268126 | c.711G>A | synonymous_variant | 0.12 |
aftB | 4268174 | c.663G>T | synonymous_variant | 0.14 |
aftB | 4268608 | p.Met77Val | missense_variant | 0.12 |
aftB | 4269249 | c.-413G>A | upstream_gene_variant | 0.15 |
ethA | 4326326 | p.Thr383Met | missense_variant | 0.13 |
ethA | 4326580 | p.Asn298Lys | missense_variant | 0.14 |
ethR | 4327884 | p.Glu112Asp | missense_variant | 0.11 |
ethA | 4328212 | c.-740delC | upstream_gene_variant | 1.0 |
whiB6 | 4338264 | c.258G>C | synonymous_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338602 | c.-81A>T | upstream_gene_variant | 0.15 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |