Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS12985

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse11; day2

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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_RS13000 and HMPREF1058_RS12995 are separated by 105 nucleotidesHMPREF1058_RS12995 and HMPREF1058_RS12990 are separated by 11 nucleotidesHMPREF1058_RS12990 and HMPREF1058_RS12985 are separated by 262 nucleotidesHMPREF1058_RS12985 and HMPREF1058_RS12980 are separated by 159 nucleotidesHMPREF1058_RS12980 and HMPREF1058_RS12975 are separated by 451 nucleotides HMPREF1058_RS13000: HMPREF1058_RS13000 - hypothetical protein, at 1,619,394 to 1,621,001 _RS13000 HMPREF1058_RS12995: HMPREF1058_RS12995 - hypothetical protein, at 1,621,107 to 1,621,388 _RS12995 HMPREF1058_RS12990: HMPREF1058_RS12990 - hypothetical protein, at 1,621,400 to 1,621,588 _RS12990 HMPREF1058_RS12985: HMPREF1058_RS12985 - DUF3871 family protein, at 1,621,851 to 1,622,897 _RS12985 HMPREF1058_RS12980: HMPREF1058_RS12980 - hypothetical protein, at 1,623,057 to 1,623,239 _RS12980 HMPREF1058_RS12975: HMPREF1058_RS12975 - hypothetical protein, at 1,623,691 to 1,623,915 _RS12975 Position (kb) 1621 1622 1623Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3 4 5at 1620.992 kb on - strandat 1621.001 kb on + strandat 1621.001 kb on + strandat 1621.002 kb on - strandat 1621.046 kb on + strandat 1621.160 kb on + strand, within HMPREF1058_RS12995at 1621.164 kb on + strand, within HMPREF1058_RS12995at 1621.164 kb on + strand, within HMPREF1058_RS12995at 1621.239 kb on - strand, within HMPREF1058_RS12995at 1621.260 kb on + strand, within HMPREF1058_RS12995at 1621.393 kb on + strandat 1621.398 kb on + strandat 1621.398 kb on + strandat 1621.398 kb on + strandat 1621.454 kb on + strand, within HMPREF1058_RS12990at 1621.454 kb on + strand, within HMPREF1058_RS12990at 1621.457 kb on - strand, within HMPREF1058_RS12990at 1621.522 kb on + strand, within HMPREF1058_RS12990at 1621.602 kb on + strandat 1621.602 kb on + strandat 1621.646 kb on + strandat 1621.690 kb on + strandat 1621.725 kb on + strandat 1621.739 kb on + strandat 1621.739 kb on + strandat 1621.960 kb on + strand, within HMPREF1058_RS12985at 1621.961 kb on - strand, within HMPREF1058_RS12985at 1622.049 kb on + strand, within HMPREF1058_RS12985at 1622.049 kb on + strand, within HMPREF1058_RS12985at 1622.049 kb on + strand, within HMPREF1058_RS12985at 1622.050 kb on - strand, within HMPREF1058_RS12985at 1622.063 kb on + strand, within HMPREF1058_RS12985at 1622.154 kb on + strand, within HMPREF1058_RS12985at 1622.155 kb on - strand, within HMPREF1058_RS12985at 1622.183 kb on + strand, within HMPREF1058_RS12985at 1622.244 kb on + strand, within HMPREF1058_RS12985at 1622.250 kb on + strand, within HMPREF1058_RS12985at 1622.251 kb on - strand, within HMPREF1058_RS12985at 1622.251 kb on - strand, within HMPREF1058_RS12985at 1622.263 kb on + strand, within HMPREF1058_RS12985at 1622.264 kb on - strand, within HMPREF1058_RS12985at 1622.265 kb on + strand, within HMPREF1058_RS12985at 1622.267 kb on + strand, within HMPREF1058_RS12985at 1622.267 kb on + strand, within HMPREF1058_RS12985at 1622.322 kb on - strand, within HMPREF1058_RS12985at 1622.392 kb on - strand, within HMPREF1058_RS12985at 1622.431 kb on - strand, within HMPREF1058_RS12985at 1622.432 kb on + strand, within HMPREF1058_RS12985at 1622.465 kb on + strand, within HMPREF1058_RS12985at 1622.466 kb on - strand, within HMPREF1058_RS12985at 1622.492 kb on + strand, within HMPREF1058_RS12985at 1622.503 kb on + strand, within HMPREF1058_RS12985at 1622.504 kb on - strand, within HMPREF1058_RS12985at 1622.504 kb on - strand, within HMPREF1058_RS12985at 1622.504 kb on - strand, within HMPREF1058_RS12985at 1622.507 kb on + strand, within HMPREF1058_RS12985at 1622.652 kb on + strand, within HMPREF1058_RS12985at 1622.653 kb on - strand, within HMPREF1058_RS12985at 1622.676 kb on - strand, within HMPREF1058_RS12985at 1622.823 kb on - strandat 1622.874 kb on - strandat 1622.898 kb on - strandat 1623.030 kb on + strandat 1623.071 kb on + strandat 1623.148 kb on + strand, within HMPREF1058_RS12980at 1623.149 kb on - strand, within HMPREF1058_RS12980at 1623.149 kb on - strand, within HMPREF1058_RS12980at 1623.263 kb on + strandat 1623.282 kb on + strandat 1623.282 kb on + strandat 1623.282 kb on + strandat 1623.286 kb on + strandat 1623.299 kb on + strandat 1623.300 kb on - strandat 1623.393 kb on + strandat 1623.529 kb on + strandat 1623.530 kb on - strandat 1623.570 kb on + strandat 1623.572 kb on + strandat 1623.572 kb on + strandat 1623.573 kb on - strandat 1623.573 kb on - strandat 1623.573 kb on - strandat 1623.574 kb on + strandat 1623.624 kb on + strandat 1623.627 kb on - strandat 1623.628 kb on + strandat 1623.629 kb on - strandat 1623.686 kb on - strandat 1623.719 kb on + strand, within HMPREF1058_RS12975at 1623.720 kb on - strand, within HMPREF1058_RS12975at 1623.737 kb on + strand, within HMPREF1058_RS12975at 1623.799 kb on + strand, within HMPREF1058_RS12975at 1623.826 kb on + strand, within HMPREF1058_RS12975at 1623.827 kb on - strand, within HMPREF1058_RS12975at 1623.842 kb on + strand, within HMPREF1058_RS12975at 1623.842 kb on + strand, within HMPREF1058_RS12975at 1623.842 kb on + strand, within HMPREF1058_RS12975at 1623.843 kb on - strand, within HMPREF1058_RS12975at 1623.843 kb on - strand, within HMPREF1058_RS12975at 1623.844 kb on + strand, within HMPREF1058_RS12975at 1623.845 kb on - strand, within HMPREF1058_RS12975at 1623.845 kb on - strand, within HMPREF1058_RS12975at 1623.846 kb on + strand, within HMPREF1058_RS12975at 1623.847 kb on - strand, within HMPREF1058_RS12975at 1623.848 kb on + strand, within HMPREF1058_RS12975at 1623.848 kb on + strand, within HMPREF1058_RS12975at 1623.849 kb on - strand, within HMPREF1058_RS12975at 1623.849 kb on - strand, within HMPREF1058_RS12975at 1623.851 kb on + strand, within HMPREF1058_RS12975at 1623.857 kb on + strand, within HMPREF1058_RS12975at 1623.892 kb on + strand, within HMPREF1058_RS12975at 1623.893 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse11; day2
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1,620,992 - -1.1
1,621,001 + +2.7
1,621,001 + +1.0
1,621,002 - +1.5
1,621,046 + +0.0
1,621,160 + HMPREF1058_RS12995 0.19 -2.0
1,621,164 + HMPREF1058_RS12995 0.20 +1.2
1,621,164 + HMPREF1058_RS12995 0.20 +0.6
1,621,239 - HMPREF1058_RS12995 0.47 +0.6
1,621,260 + HMPREF1058_RS12995 0.54 +0.5
1,621,393 + +0.6
1,621,398 + +0.6
1,621,398 + -1.9
1,621,398 + +0.3
1,621,454 + HMPREF1058_RS12990 0.29 +1.6
1,621,454 + HMPREF1058_RS12990 0.29 +0.0
1,621,457 - HMPREF1058_RS12990 0.30 +0.0
1,621,522 + HMPREF1058_RS12990 0.65 -2.6
1,621,602 + +0.0
1,621,602 + +2.3
1,621,646 + -2.3
1,621,690 + +1.8
1,621,725 + +1.0
1,621,739 + -1.3
1,621,739 + +0.1
1,621,960 + HMPREF1058_RS12985 0.10 +1.8
1,621,961 - HMPREF1058_RS12985 0.11 -2.8
1,622,049 + HMPREF1058_RS12985 0.19 +0.7
1,622,049 + HMPREF1058_RS12985 0.19 +0.8
1,622,049 + HMPREF1058_RS12985 0.19 +0.0
1,622,050 - HMPREF1058_RS12985 0.19 +0.4
1,622,063 + HMPREF1058_RS12985 0.20 -0.2
1,622,154 + HMPREF1058_RS12985 0.29 -2.0
1,622,155 - HMPREF1058_RS12985 0.29 +1.2
1,622,183 + HMPREF1058_RS12985 0.32 -1.0
1,622,244 + HMPREF1058_RS12985 0.38 -1.0
1,622,250 + HMPREF1058_RS12985 0.38 -2.0
1,622,251 - HMPREF1058_RS12985 0.38 +0.5
1,622,251 - HMPREF1058_RS12985 0.38 -1.9
1,622,263 + HMPREF1058_RS12985 0.39 -1.2
1,622,264 - HMPREF1058_RS12985 0.39 +1.6
1,622,265 + HMPREF1058_RS12985 0.40 +0.0
1,622,267 + HMPREF1058_RS12985 0.40 +4.9
1,622,267 + HMPREF1058_RS12985 0.40 +0.2
1,622,322 - HMPREF1058_RS12985 0.45 +1.9
1,622,392 - HMPREF1058_RS12985 0.52 -1.0
1,622,431 - HMPREF1058_RS12985 0.55 -1.0
1,622,432 + HMPREF1058_RS12985 0.55 -1.6
1,622,465 + HMPREF1058_RS12985 0.59 +0.0
1,622,466 - HMPREF1058_RS12985 0.59 -2.2
1,622,492 + HMPREF1058_RS12985 0.61 +0.3
1,622,503 + HMPREF1058_RS12985 0.62 +0.8
1,622,504 - HMPREF1058_RS12985 0.62 +1.3
1,622,504 - HMPREF1058_RS12985 0.62 +1.0
1,622,504 - HMPREF1058_RS12985 0.62 +0.4
1,622,507 + HMPREF1058_RS12985 0.63 +2.3
1,622,652 + HMPREF1058_RS12985 0.77 -0.2
1,622,653 - HMPREF1058_RS12985 0.77 +0.0
1,622,676 - HMPREF1058_RS12985 0.79 -0.8
1,622,823 - -0.6
1,622,874 - +0.0
1,622,898 - -0.6
1,623,030 + +0.5
1,623,071 + -1.6
1,623,148 + HMPREF1058_RS12980 0.50 +0.3
1,623,149 - HMPREF1058_RS12980 0.50 +1.0
1,623,149 - HMPREF1058_RS12980 0.50 +1.8
1,623,263 + -0.6
1,623,282 + -1.2
1,623,282 + +1.3
1,623,282 + -4.4
1,623,286 + +0.5
1,623,299 + -0.4
1,623,300 - -2.0
1,623,393 + +0.0
1,623,529 + +0.0
1,623,530 - +0.4
1,623,570 + -1.0
1,623,572 + -1.0
1,623,572 + +0.3
1,623,573 - +0.4
1,623,573 - +0.7
1,623,573 - +0.7
1,623,574 + -0.4
1,623,624 + -1.6
1,623,627 - +3.0
1,623,628 + -0.6
1,623,629 - +2.3
1,623,686 - -2.1
1,623,719 + HMPREF1058_RS12975 0.12 +0.8
1,623,720 - HMPREF1058_RS12975 0.13 +1.5
1,623,737 + HMPREF1058_RS12975 0.20 -0.4
1,623,799 + HMPREF1058_RS12975 0.48 +1.0
1,623,826 + HMPREF1058_RS12975 0.60 -2.0
1,623,827 - HMPREF1058_RS12975 0.60 +0.7
1,623,842 + HMPREF1058_RS12975 0.67 +1.8
1,623,842 + HMPREF1058_RS12975 0.67 +1.7
1,623,842 + HMPREF1058_RS12975 0.67 +0.0
1,623,843 - HMPREF1058_RS12975 0.68 +1.0
1,623,843 - HMPREF1058_RS12975 0.68 +2.8
1,623,844 + HMPREF1058_RS12975 0.68 +1.5
1,623,845 - HMPREF1058_RS12975 0.68 +1.1
1,623,845 - HMPREF1058_RS12975 0.68 -2.3
1,623,846 + HMPREF1058_RS12975 0.69 +2.7
1,623,847 - HMPREF1058_RS12975 0.69 +1.3
1,623,848 + HMPREF1058_RS12975 0.70 +1.7
1,623,848 + HMPREF1058_RS12975 0.70 +1.5
1,623,849 - HMPREF1058_RS12975 0.70 -1.2
1,623,849 - HMPREF1058_RS12975 0.70 +0.7
1,623,851 + HMPREF1058_RS12975 0.71 +2.8
1,623,857 + HMPREF1058_RS12975 0.74 +1.0
1,623,892 + HMPREF1058_RS12975 0.89 +2.2
1,623,893 - +0.8

Or see this region's nucleotide sequence