Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 345,099 C→T 9.6% A155T (GCC→ACC)  yahN ← neutral amino‑acid efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb345,0990CT 9.6% 156.9 / 6.4 52A155T (GCC→ACC) yahNneutral amino‑acid efflux system
Reads supporting (aligned to +/- strand):  ref base C (25/22);  new base T (2/3);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 6.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-01

AGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGTAATTA  >  W3110S.gb/345036‑345167
                                                               |                                                                    
aGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAAt                                                               >  1:2880111/1‑71 (MQ=255)
 gATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAt                                                                    >  1:3231888/1‑65 (MQ=255)
 gATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATg                                                              >  1:2392713/1‑71 (MQ=255)
  aTAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGt                                                             <  1:4113673/71‑1 (MQ=255)
   tAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGtt                                                            <  1:3039580/71‑1 (MQ=255)
    aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                           >  1:4262694/1‑71 (MQ=255)
    aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                           >  1:2294148/1‑71 (MQ=255)
        gATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACt                                                         >  1:804152/1‑69 (MQ=255)
           gCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATg                                                              >  1:1374524/1‑61 (MQ=255)
            cGAGCACAATCCCCGGCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaa                                                    >  1:2481156/1‑70 (MQ=255)
            cGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAt                                                                    >  1:2041692/1‑54 (MQ=255)
             gAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGaaaa                                                  <  1:2129334/71‑1 (MQ=255)
              aGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa                                                  <  1:3895902/70‑1 (MQ=255)
               gCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATa                                                >  1:3056279/1‑71 (MQ=255)
                 acaATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACt                                              <  1:621890/71‑1 (MQ=255)
                    aTCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGtt                                                            <  1:4062115/54‑1 (MQ=255)
                         cGCCAAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGATaaaaa                                      <  1:1101450/71‑1 (MQ=255)
                          gCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATATAAAGTTACTGAGAAAATAc                                               >  1:262517/1‑61 (MQ=255)
                           cccAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATa                                                >  1:3103001/1‑59 (MQ=255)
                           cccAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAAt                                    <  1:3057225/71‑1 (MQ=255)
                             cAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTa                                                                 <  1:1431125/40‑1 (MQ=255)
                             cAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaa                                  <  1:2240190/71‑1 (MQ=255)
                             cAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaa                                  <  1:1659557/71‑1 (MQ=255)
                                 ccATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATaaaaaa                                     >  1:607402/1‑64 (MQ=255)
                                 ccATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATaaaaaa                                     >  1:813179/1‑64 (MQ=255)
                                  cATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACg                              >  1:939924/1‑70 (MQ=255)
                                    ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTgag                                                      <  1:856777/44‑1 (MQ=255)
                                    ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa                                                  <  1:1325513/48‑1 (MQ=255)
                                    ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaa                                                    <  1:2500948/46‑1 (MQ=255)
                                    ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGtt                           <  1:4073627/71‑1 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGa                                            >  1:418995/1‑52 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                           >  1:1152013/1‑37 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                           >  1:499203/1‑37 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                           >  1:197159/1‑37 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaa                                                   >  1:3845383/1‑45 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATa                                                >  1:1703471/1‑48 (MQ=255)
                                      aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTg                         >  1:905027/1‑71 (MQ=255)
                                       aaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGc                        >  1:2690491/1‑71 (MQ=255)
                                              ccATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa                                                  <  1:450591/38‑1 (MQ=255)
                                              ccATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTTCGGGTTa                  <  1:1715997/70‑1 (MQ=255)
                                                aTGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAAt                                    <  1:2949946/50‑1 (MQ=255)
                                                aTGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAAt                                    <  1:2932539/50‑1 (MQ=255)
                                                aTGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTagag               <  1:408347/71‑1 (MQ=255)
                                                 tGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaaaa                                >  1:3978929/1‑53 (MQ=255)
                                                 tGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaaaa                                >  1:1377087/1‑53 (MQ=255)
                                                 tGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCg                       <  1:3627559/62‑1 (MQ=255)
                                                    tGGTGTTTCGGCATTTAATGTTACTGAGAAAATAc                                               >  1:1105675/1‑35 (MQ=255)
                                                     ggTGTTTCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGAt           <  1:322381/70‑1 (MQ=255)
                                                         tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga                <  1:4004250/61‑1 (MQ=255)
                                                          ttCGGCATTTAATGTTACTGAGAAAATACTGATaaaa                                       <  1:4252383/37‑1 (MQ=255)
                                                           tCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTa                  >  1:286790/1‑57 (MQ=255)
                                                             ggCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGtaatta  <  1:2365247/71‑1 (MQ=255)
                                                               cATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt       <  1:384467/64‑1 (MQ=255)
                                                               |                                                                    
AGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGTAATTA  >  W3110S.gb/345036‑345167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A