Strain Fitness in Parabacteroides merdae CL09T00C40 around HMPREF1078_RS05930

Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; day4

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Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

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500 ntHMPREF1078_RS05920 and HMPREF1078_RS05925 are separated by 12 nucleotidesHMPREF1078_RS05925 and HMPREF1078_RS05930 are separated by 16 nucleotidesHMPREF1078_RS05930 and HMPREF1078_RS05935 overlap by 4 nucleotidesHMPREF1078_RS05935 and HMPREF1078_RS05940 are separated by 118 nucleotides HMPREF1078_RS05920: HMPREF1078_RS05920 - RNA polymerase factor sigma-54, at 518,725 to 520,194 _RS05920 HMPREF1078_RS05925: HMPREF1078_RS05925 - hypothetical protein, at 520,207 to 520,827 _RS05925 HMPREF1078_RS05930: HMPREF1078_RS05930 - glycine cleavage system protein GcvH, at 520,844 to 521,224 _RS05930 HMPREF1078_RS05935: HMPREF1078_RS05935 - 5-(carboxyamino)imidazole ribonucleotide mutase, at 521,221 to 521,727 _RS05935 HMPREF1078_RS05940: HMPREF1078_RS05940 - 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, at 521,846 to 523,687 _RS05940 Position (kb) 520 521 522Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 519.855 kb on + strand, within HMPREF1078_RS05920at 519.872 kb on + strand, within HMPREF1078_RS05920at 519.897 kb on - strand, within HMPREF1078_RS05920at 519.932 kb on + strand, within HMPREF1078_RS05920at 520.046 kb on + strand, within HMPREF1078_RS05920at 520.115 kb on - strandat 520.116 kb on + strandat 520.117 kb on - strandat 520.207 kb on - strandat 520.224 kb on + strandat 520.224 kb on + strandat 520.225 kb on - strandat 520.225 kb on - strandat 520.264 kb on + strandat 520.264 kb on + strandat 520.264 kb on + strandat 520.264 kb on + strandat 520.265 kb on - strandat 520.265 kb on - strandat 520.294 kb on + strand, within HMPREF1078_RS05925at 520.391 kb on + strand, within HMPREF1078_RS05925at 520.421 kb on + strand, within HMPREF1078_RS05925at 520.451 kb on - strand, within HMPREF1078_RS05925at 520.490 kb on - strand, within HMPREF1078_RS05925at 520.492 kb on - strand, within HMPREF1078_RS05925at 520.492 kb on - strand, within HMPREF1078_RS05925at 520.492 kb on - strand, within HMPREF1078_RS05925at 520.492 kb on - strand, within HMPREF1078_RS05925at 520.492 kb on - strand, within HMPREF1078_RS05925at 520.495 kb on + strand, within HMPREF1078_RS05925at 520.495 kb on + strand, within HMPREF1078_RS05925at 520.496 kb on - strand, within HMPREF1078_RS05925at 520.496 kb on - strand, within HMPREF1078_RS05925at 520.497 kb on + strand, within HMPREF1078_RS05925at 520.498 kb on - strand, within HMPREF1078_RS05925at 520.565 kb on + strand, within HMPREF1078_RS05925at 520.565 kb on + strand, within HMPREF1078_RS05925at 520.566 kb on - strand, within HMPREF1078_RS05925at 520.622 kb on + strand, within HMPREF1078_RS05925at 520.622 kb on + strand, within HMPREF1078_RS05925at 520.622 kb on + strand, within HMPREF1078_RS05925at 520.622 kb on + strand, within HMPREF1078_RS05925at 520.622 kb on + strand, within HMPREF1078_RS05925at 520.623 kb on - strand, within HMPREF1078_RS05925at 520.623 kb on - strand, within HMPREF1078_RS05925at 520.629 kb on + strand, within HMPREF1078_RS05925at 520.659 kb on - strand, within HMPREF1078_RS05925at 520.691 kb on + strand, within HMPREF1078_RS05925at 520.691 kb on + strand, within HMPREF1078_RS05925at 520.692 kb on - strand, within HMPREF1078_RS05925at 520.737 kb on + strand, within HMPREF1078_RS05925at 520.738 kb on - strand, within HMPREF1078_RS05925at 520.743 kb on + strand, within HMPREF1078_RS05925at 520.751 kb on + strand, within HMPREF1078_RS05925at 520.751 kb on + strand, within HMPREF1078_RS05925at 520.752 kb on - strand, within HMPREF1078_RS05925at 520.752 kb on - strand, within HMPREF1078_RS05925at 520.753 kb on + strand, within HMPREF1078_RS05925at 520.753 kb on + strand, within HMPREF1078_RS05925at 520.753 kb on + strand, within HMPREF1078_RS05925at 520.754 kb on - strand, within HMPREF1078_RS05925at 520.754 kb on - strand, within HMPREF1078_RS05925at 520.776 kb on + strandat 520.778 kb on + strandat 520.782 kb on + strandat 520.782 kb on + strandat 520.809 kb on + strandat 520.809 kb on + strandat 520.817 kb on + strandat 520.863 kb on + strandat 520.863 kb on + strandat 520.896 kb on + strand, within HMPREF1078_RS05930at 520.921 kb on + strand, within HMPREF1078_RS05930at 520.924 kb on + strand, within HMPREF1078_RS05930at 520.931 kb on + strand, within HMPREF1078_RS05930at 521.028 kb on + strand, within HMPREF1078_RS05930at 521.046 kb on + strand, within HMPREF1078_RS05930at 521.046 kb on + strand, within HMPREF1078_RS05930at 521.124 kb on + strand, within HMPREF1078_RS05930at 521.124 kb on + strand, within HMPREF1078_RS05930at 521.124 kb on + strand, within HMPREF1078_RS05930at 521.124 kb on + strand, within HMPREF1078_RS05930at 521.124 kb on + strand, within HMPREF1078_RS05930at 521.126 kb on + strand, within HMPREF1078_RS05930at 521.151 kb on + strand, within HMPREF1078_RS05930at 521.151 kb on + strand, within HMPREF1078_RS05930at 521.201 kb on + strandat 521.241 kb on + strandat 521.253 kb on + strandat 521.253 kb on + strandat 521.343 kb on + strand, within HMPREF1078_RS05935at 521.586 kb on + strand, within HMPREF1078_RS05935at 521.586 kb on + strand, within HMPREF1078_RS05935at 521.647 kb on + strand, within HMPREF1078_RS05935at 521.647 kb on + strand, within HMPREF1078_RS05935at 521.715 kb on + strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; day4
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519,855 + HMPREF1078_RS05920 0.77 -0.5
519,872 + HMPREF1078_RS05920 0.78 +1.1
519,897 - HMPREF1078_RS05920 0.80 +1.1
519,932 + HMPREF1078_RS05920 0.82 +1.1
520,046 + HMPREF1078_RS05920 0.90 -0.5
520,115 - -2.2
520,116 + -0.5
520,117 - -0.5
520,207 - +2.1
520,224 + -0.6
520,224 + -0.1
520,225 - +0.9
520,225 - -0.2
520,264 + +0.1
520,264 + +0.1
520,264 + -0.5
520,264 + -2.4
520,265 - +0.3
520,265 - -1.6
520,294 + HMPREF1078_RS05925 0.14 +1.1
520,391 + HMPREF1078_RS05925 0.30 -2.2
520,421 + HMPREF1078_RS05925 0.34 -0.7
520,451 - HMPREF1078_RS05925 0.39 -0.0
520,490 - HMPREF1078_RS05925 0.46 +0.6
520,492 - HMPREF1078_RS05925 0.46 -1.5
520,492 - HMPREF1078_RS05925 0.46 +0.6
520,492 - HMPREF1078_RS05925 0.46 +0.5
520,492 - HMPREF1078_RS05925 0.46 +0.3
520,492 - HMPREF1078_RS05925 0.46 -1.9
520,495 + HMPREF1078_RS05925 0.46 -3.0
520,495 + HMPREF1078_RS05925 0.46 +0.8
520,496 - HMPREF1078_RS05925 0.47 -1.7
520,496 - HMPREF1078_RS05925 0.47 -1.5
520,497 + HMPREF1078_RS05925 0.47 -1.3
520,498 - HMPREF1078_RS05925 0.47 +0.8
520,565 + HMPREF1078_RS05925 0.58 -2.8
520,565 + HMPREF1078_RS05925 0.58 +1.5
520,566 - HMPREF1078_RS05925 0.58 +0.4
520,622 + HMPREF1078_RS05925 0.67 -2.4
520,622 + HMPREF1078_RS05925 0.67 -2.2
520,622 + HMPREF1078_RS05925 0.67 +2.1
520,622 + HMPREF1078_RS05925 0.67 -1.3
520,622 + HMPREF1078_RS05925 0.67 -1.4
520,623 - HMPREF1078_RS05925 0.67 -0.9
520,623 - HMPREF1078_RS05925 0.67 +0.3
520,629 + HMPREF1078_RS05925 0.68 +0.9
520,659 - HMPREF1078_RS05925 0.73 -0.5
520,691 + HMPREF1078_RS05925 0.78 +1.5
520,691 + HMPREF1078_RS05925 0.78 -1.5
520,692 - HMPREF1078_RS05925 0.78 -0.3
520,737 + HMPREF1078_RS05925 0.85 -0.5
520,738 - HMPREF1078_RS05925 0.86 +1.3
520,743 + HMPREF1078_RS05925 0.86 -1.0
520,751 + HMPREF1078_RS05925 0.88 -1.5
520,751 + HMPREF1078_RS05925 0.88 +0.6
520,752 - HMPREF1078_RS05925 0.88 -0.5
520,752 - HMPREF1078_RS05925 0.88 -0.8
520,753 + HMPREF1078_RS05925 0.88 +0.4
520,753 + HMPREF1078_RS05925 0.88 -0.0
520,753 + HMPREF1078_RS05925 0.88 -0.5
520,754 - HMPREF1078_RS05925 0.88 -3.4
520,754 - HMPREF1078_RS05925 0.88 -3.5
520,776 + +0.3
520,778 + +0.3
520,782 + -0.9
520,782 + +0.9
520,809 + -0.3
520,809 + -0.9
520,817 + +1.1
520,863 + -2.7
520,863 + -3.3
520,896 + HMPREF1078_RS05930 0.14 -3.1
520,921 + HMPREF1078_RS05930 0.20 -3.0
520,924 + HMPREF1078_RS05930 0.21 -2.9
520,931 + HMPREF1078_RS05930 0.23 -0.6
521,028 + HMPREF1078_RS05930 0.48 -1.9
521,046 + HMPREF1078_RS05930 0.53 -3.4
521,046 + HMPREF1078_RS05930 0.53 -3.0
521,124 + HMPREF1078_RS05930 0.73 -2.4
521,124 + HMPREF1078_RS05930 0.73 -2.5
521,124 + HMPREF1078_RS05930 0.73 -1.3
521,124 + HMPREF1078_RS05930 0.73 -0.8
521,124 + HMPREF1078_RS05930 0.73 +0.1
521,126 + HMPREF1078_RS05930 0.74 -1.5
521,151 + HMPREF1078_RS05930 0.81 -2.1
521,151 + HMPREF1078_RS05930 0.81 +0.3
521,201 + -0.6
521,241 + -2.5
521,253 + -3.6
521,253 + -3.6
521,343 + HMPREF1078_RS05935 0.24 -3.3
521,586 + HMPREF1078_RS05935 0.72 -1.5
521,586 + HMPREF1078_RS05935 0.72 -3.6
521,647 + HMPREF1078_RS05935 0.84 -1.5
521,647 + HMPREF1078_RS05935 0.84 -1.7
521,715 + -2.2

Or see this region's nucleotide sequence