Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS18960

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse20; day9

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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 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) 40 41 42Strain fitness (log2 ratio) -2 -1 0 1 2 3 4at 39.857 kb on - strandat 39.857 kb on - strandat 39.892 kb on + strandat 39.893 kb on - strandat 39.915 kb on - strandat 39.997 kb on - strandat 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 - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse20; day9
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39,857 - -1.9
39,857 - -0.6
39,892 + -2.6
39,893 - +1.0
39,915 - -0.0
39,997 - +0.3
40,073 + +0.6
40,073 + +0.5
40,122 + +0.6
40,122 + +0.6
40,123 - -1.6
40,123 - -0.1
40,126 + -0.4
40,173 + -1.0
40,209 + -0.5
40,233 - +0.2
40,333 - HMPREF1058_RS18970 0.35 -0.7
40,338 - HMPREF1058_RS18970 0.36 +0.7
40,372 + HMPREF1058_RS18970 0.45 -0.3
40,372 + HMPREF1058_RS18970 0.45 -2.7
40,372 + HMPREF1058_RS18970 0.45 -0.2
40,372 + HMPREF1058_RS18970 0.45 -2.3
40,373 - HMPREF1058_RS18970 0.45 -2.0
40,427 + HMPREF1058_RS18970 0.59 +1.6
40,428 - HMPREF1058_RS18970 0.59 -0.2
40,466 + HMPREF1058_RS18970 0.68 +0.4
40,468 + HMPREF1058_RS18970 0.69 +0.1
40,512 - HMPREF1058_RS18970 0.80 +0.6
40,516 - HMPREF1058_RS18970 0.81 +0.1
40,561 - +0.6
40,606 - -0.1
40,606 - -1.7
40,650 + +0.5
40,651 - -0.2
40,784 - -1.2
40,801 + +0.1
40,802 - -1.5
40,810 - +0.2
40,814 + -0.9
40,833 + -0.6
40,871 + HMPREF1058_RS18960 0.15 +1.0
40,886 - HMPREF1058_RS18960 0.22 +0.4
40,912 + HMPREF1058_RS18960 0.35 +1.1
40,936 - HMPREF1058_RS18960 0.47 +3.8
40,940 - HMPREF1058_RS18960 0.49 -1.3
40,954 + HMPREF1058_RS18960 0.55 -0.7
40,997 - HMPREF1058_RS18960 0.76 +0.6
41,026 + +1.4
41,026 + +0.3
41,031 - +0.4
41,031 - -0.1
41,033 + -0.5
41,035 + -1.5
41,035 + -0.0
41,036 - -2.2
41,096 - HMPREF1058_RS18955 0.13 -1.9
41,099 - HMPREF1058_RS18955 0.14 -2.0
41,141 + HMPREF1058_RS18955 0.26 -0.5
41,207 - HMPREF1058_RS18955 0.44 -2.6
41,207 - HMPREF1058_RS18955 0.44 +0.1
41,207 - HMPREF1058_RS18955 0.44 -0.2
41,208 + HMPREF1058_RS18955 0.44 -1.0
41,209 - HMPREF1058_RS18955 0.45 +0.4
41,209 - HMPREF1058_RS18955 0.45 -0.6
41,210 + HMPREF1058_RS18955 0.45 -0.9
41,210 + HMPREF1058_RS18955 0.45 -0.1
41,210 + HMPREF1058_RS18955 0.45 +0.5
41,210 + HMPREF1058_RS18955 0.45 -2.7
41,213 - HMPREF1058_RS18955 0.46 +0.4
41,334 - HMPREF1058_RS18955 0.79 -0.9
41,478 + +0.1
41,528 + +1.1
41,529 - -1.3
41,615 + -0.3
41,648 + HMPREF1058_RS20355 0.12 +1.1
41,649 - HMPREF1058_RS20355 0.12 +0.1
41,810 + HMPREF1058_RS20355 0.63 -0.2
41,811 - HMPREF1058_RS20355 0.63 -1.0
41,811 - HMPREF1058_RS20355 0.63 +0.1
41,842 + HMPREF1058_RS20355 0.73 +0.1
41,917 + -1.0
41,985 + -1.9
42,018 + -0.0
42,032 - -0.5

Or see this region's nucleotide sequence