Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS18955

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse11; day3

Add experiment(s):

Zoom: Pan:

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.

download SVG
500 ntHMPREF1058_RS18970 and HMPREF1058_RS18960 are separated by 251 nucleotidesHMPREF1058_RS18960 and HMPREF1058_RS18955 are separated by 2 nucleotidesHMPREF1058_RS18955 and HMPREF1058_RS20355 are separated by 200 nucleotidesHMPREF1058_RS20355 and HMPREF1058_RS18945 overlap by 4 nucleotides HMPREF1058_RS18970: HMPREF1058_RS18970 - hypothetical protein, at 40,197 to 40,589 _RS18970 HMPREF1058_RS18960: HMPREF1058_RS18960 - hypothetical protein, at 40,841 to 41,044 _RS18960 HMPREF1058_RS18955: HMPREF1058_RS18955 - DUF551 domain-containing protein, at 41,047 to 41,409 _RS18955 HMPREF1058_RS20355: HMPREF1058_RS20355 - hypothetical protein, at 41,610 to 41,927 _RS20355 HMPREF1058_RS18945: HMPREF1058_RS18945 - DNA methylase N-4, at 41,924 to 44,440 _RS18945 Position (kb) 41 42Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3 4at 40.073 kb on + strandat 40.073 kb on + strandat 40.122 kb on + strandat 40.122 kb on + strandat 40.123 kb on - strandat 40.123 kb on - strandat 40.126 kb on + strandat 40.173 kb on + strandat 40.209 kb on + strandat 40.233 kb on - strandat 40.333 kb on - strand, within HMPREF1058_RS18970at 40.338 kb on - strand, within HMPREF1058_RS18970at 40.372 kb on + strand, within HMPREF1058_RS18970at 40.372 kb on + strand, within HMPREF1058_RS18970at 40.372 kb on + strand, within HMPREF1058_RS18970at 40.372 kb on + strand, within HMPREF1058_RS18970at 40.373 kb on - strand, within HMPREF1058_RS18970at 40.427 kb on + strand, within HMPREF1058_RS18970at 40.428 kb on - strand, within HMPREF1058_RS18970at 40.466 kb on + strand, within HMPREF1058_RS18970at 40.468 kb on + strand, within HMPREF1058_RS18970at 40.512 kb on - strand, within HMPREF1058_RS18970at 40.516 kb on - strand, within HMPREF1058_RS18970at 40.561 kb on - strandat 40.606 kb on - strandat 40.606 kb on - strandat 40.650 kb on + strandat 40.651 kb on - strandat 40.784 kb on - strandat 40.801 kb on + strandat 40.802 kb on - strandat 40.810 kb on - strandat 40.814 kb on + strandat 40.833 kb on + strandat 40.871 kb on + strand, within HMPREF1058_RS18960at 40.886 kb on - strand, within HMPREF1058_RS18960at 40.912 kb on + strand, within HMPREF1058_RS18960at 40.936 kb on - strand, within HMPREF1058_RS18960at 40.940 kb on - strand, within HMPREF1058_RS18960at 40.954 kb on + strand, within HMPREF1058_RS18960at 40.997 kb on - strand, within HMPREF1058_RS18960at 41.026 kb on + strandat 41.026 kb on + strandat 41.031 kb on - strandat 41.031 kb on - strandat 41.033 kb on + strandat 41.035 kb on + strandat 41.035 kb on + strandat 41.036 kb on - strandat 41.096 kb on - strand, within HMPREF1058_RS18955at 41.099 kb on - strand, within HMPREF1058_RS18955at 41.141 kb on + strand, within HMPREF1058_RS18955at 41.207 kb on - strand, within HMPREF1058_RS18955at 41.207 kb on - strand, within HMPREF1058_RS18955at 41.207 kb on - strand, within HMPREF1058_RS18955at 41.208 kb on + strand, within HMPREF1058_RS18955at 41.209 kb on - strand, within HMPREF1058_RS18955at 41.209 kb on - strand, within HMPREF1058_RS18955at 41.210 kb on + strand, within HMPREF1058_RS18955at 41.210 kb on + strand, within HMPREF1058_RS18955at 41.210 kb on + strand, within HMPREF1058_RS18955at 41.210 kb on + strand, within HMPREF1058_RS18955at 41.213 kb on - strand, within HMPREF1058_RS18955at 41.334 kb on - strand, within HMPREF1058_RS18955at 41.478 kb on + strandat 41.528 kb on + strandat 41.529 kb on - strandat 41.615 kb on + strandat 41.648 kb on + strand, within HMPREF1058_RS20355at 41.649 kb on - strand, within HMPREF1058_RS20355at 41.810 kb on + strand, within HMPREF1058_RS20355at 41.811 kb on - strand, within HMPREF1058_RS20355at 41.811 kb on - strand, within HMPREF1058_RS20355at 41.842 kb on + strand, within HMPREF1058_RS20355at 41.917 kb on + strandat 41.985 kb on + strandat 42.018 kb on + strandat 42.032 kb on - strandat 42.071 kb on + strandat 42.071 kb on + strandat 42.321 kb on - strand, within HMPREF1058_RS18945at 42.337 kb on + strand, within HMPREF1058_RS18945at 42.337 kb on + strand, within HMPREF1058_RS18945at 42.338 kb on - strand, within HMPREF1058_RS18945at 42.339 kb on + strand, within HMPREF1058_RS18945at 42.339 kb on + strand, within HMPREF1058_RS18945at 42.339 kb on + strand, within HMPREF1058_RS18945at 42.339 kb on + strand, within HMPREF1058_RS18945at 42.340 kb on - strand, within HMPREF1058_RS18945at 42.340 kb on - strand, within HMPREF1058_RS18945at 42.341 kb on + strand, within HMPREF1058_RS18945at 42.341 kb on + strand, within HMPREF1058_RS18945at 42.342 kb on - strand, within HMPREF1058_RS18945at 42.342 kb on - strand, within HMPREF1058_RS18945at 42.342 kb on - strand, within HMPREF1058_RS18945at 42.343 kb on + strand, within HMPREF1058_RS18945at 42.343 kb on + strand, within HMPREF1058_RS18945at 42.382 kb on + strand, within HMPREF1058_RS18945at 42.382 kb on + strand, within HMPREF1058_RS18945at 42.382 kb on + strand, within HMPREF1058_RS18945at 42.382 kb on + strand, within HMPREF1058_RS18945at 42.383 kb on - strand, within HMPREF1058_RS18945at 42.387 kb on - strand, within HMPREF1058_RS18945

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse11; day3
remove
40,073 + -1.8
40,073 + +1.4
40,122 + +0.5
40,122 + -0.4
40,123 - +1.2
40,123 - +4.6
40,126 + +2.0
40,173 + -0.9
40,209 + -1.4
40,233 - +1.2
40,333 - HMPREF1058_RS18970 0.35 +1.6
40,338 - HMPREF1058_RS18970 0.36 -0.6
40,372 + HMPREF1058_RS18970 0.45 +0.2
40,372 + HMPREF1058_RS18970 0.45 -1.5
40,372 + HMPREF1058_RS18970 0.45 -1.8
40,372 + HMPREF1058_RS18970 0.45 -0.8
40,373 - HMPREF1058_RS18970 0.45 -1.3
40,427 + HMPREF1058_RS18970 0.59 +1.2
40,428 - HMPREF1058_RS18970 0.59 +0.1
40,466 + HMPREF1058_RS18970 0.68 -2.0
40,468 + HMPREF1058_RS18970 0.69 +0.5
40,512 - HMPREF1058_RS18970 0.80 +0.2
40,516 - HMPREF1058_RS18970 0.81 -2.3
40,561 - -0.8
40,606 - +2.4
40,606 - +0.2
40,650 + +0.3
40,651 - +1.5
40,784 - -1.7
40,801 + +2.1
40,802 - -0.8
40,810 - -0.7
40,814 + +0.9
40,833 + -3.3
40,871 + HMPREF1058_RS18960 0.15 -1.9
40,886 - HMPREF1058_RS18960 0.22 +0.2
40,912 + HMPREF1058_RS18960 0.35 -0.3
40,936 - HMPREF1058_RS18960 0.47 -0.4
40,940 - HMPREF1058_RS18960 0.49 -1.8
40,954 + HMPREF1058_RS18960 0.55 +1.8
40,997 - HMPREF1058_RS18960 0.76 +1.0
41,026 + +2.4
41,026 + +1.5
41,031 - -0.6
41,031 - -0.5
41,033 + -0.6
41,035 + -0.8
41,035 + +0.1
41,036 - +1.1
41,096 - HMPREF1058_RS18955 0.13 -2.4
41,099 - HMPREF1058_RS18955 0.14 -0.1
41,141 + HMPREF1058_RS18955 0.26 +0.8
41,207 - HMPREF1058_RS18955 0.44 -2.1
41,207 - HMPREF1058_RS18955 0.44 -2.4
41,207 - HMPREF1058_RS18955 0.44 -0.8
41,208 + HMPREF1058_RS18955 0.44 -0.3
41,209 - HMPREF1058_RS18955 0.45 -0.8
41,209 - HMPREF1058_RS18955 0.45 -0.4
41,210 + HMPREF1058_RS18955 0.45 +1.4
41,210 + HMPREF1058_RS18955 0.45 -0.5
41,210 + HMPREF1058_RS18955 0.45 -2.1
41,210 + HMPREF1058_RS18955 0.45 -2.7
41,213 - HMPREF1058_RS18955 0.46 -1.4
41,334 - HMPREF1058_RS18955 0.79 +0.2
41,478 + +0.2
41,528 + +0.7
41,529 - -2.1
41,615 + +3.6
41,648 + HMPREF1058_RS20355 0.12 +3.6
41,649 - HMPREF1058_RS20355 0.12 -0.8
41,810 + HMPREF1058_RS20355 0.63 +0.5
41,811 - HMPREF1058_RS20355 0.63 -1.6
41,811 - HMPREF1058_RS20355 0.63 +0.2
41,842 + HMPREF1058_RS20355 0.73 -1.0
41,917 + -0.4
41,985 + -0.6
42,018 + +0.2
42,032 - -1.4
42,071 + -0.2
42,071 + -2.1
42,321 - HMPREF1058_RS18945 0.16 +0.2
42,337 + HMPREF1058_RS18945 0.16 +0.0
42,337 + HMPREF1058_RS18945 0.16 +0.2
42,338 - HMPREF1058_RS18945 0.16 -1.8
42,339 + HMPREF1058_RS18945 0.16 +0.0
42,339 + HMPREF1058_RS18945 0.16 -1.4
42,339 + HMPREF1058_RS18945 0.16 +0.8
42,339 + HMPREF1058_RS18945 0.16 +1.2
42,340 - HMPREF1058_RS18945 0.17 -0.8
42,340 - HMPREF1058_RS18945 0.17 -2.4
42,341 + HMPREF1058_RS18945 0.17 -3.8
42,341 + HMPREF1058_RS18945 0.17 -0.4
42,342 - HMPREF1058_RS18945 0.17 +0.2
42,342 - HMPREF1058_RS18945 0.17 +1.1
42,342 - HMPREF1058_RS18945 0.17 +0.2
42,343 + HMPREF1058_RS18945 0.17 -0.8
42,343 + HMPREF1058_RS18945 0.17 +0.4
42,382 + HMPREF1058_RS18945 0.18 -3.3
42,382 + HMPREF1058_RS18945 0.18 -0.3
42,382 + HMPREF1058_RS18945 0.18 +1.2
42,382 + HMPREF1058_RS18945 0.18 +0.6
42,383 - HMPREF1058_RS18945 0.18 -1.0
42,387 - HMPREF1058_RS18945 0.18 -2.0

Or see this region's nucleotide sequence