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
A19 F18 I0 R2 154 40.2 915694 90.3% 826871 140.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 34.4% intergenic (‑30/‑493) tpn ← / → USA300HOU_0028 IS431mec transposase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,5810CT34.4% 78.5 / 44.4 58intergenic (‑30/‑493)tpn/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (27/11);  new base T (9/11);  total (36/22)
Fisher's exact test for biased strand distribution p-value = 8.65e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01

TTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTAT  >  CP000730/36441‑36710
                                                                                                                                             |                                                                                                                                 
ttCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGCAGACTCCTTTTTGTT‑AAAATTATAc                                                                                                                                   <  2:353262/141‑1 (MQ=17)
     ttAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATaa                                                                                                                              >  2:206968/1‑141 (MQ=33)
        atatTTCAGATATATCACAATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAAtt                                                                                                                           <  2:264455/141‑1 (MQ=25)
                      tCACGATAGCTCAATGAATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAg                                                                                                             >  1:441216/1‑141 (MQ=12)
                         cgagagcTCAATGCATATCTTAGTTAGTAGCCAACGTCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCAGACTGAAGACTCCTTTTGGTT‑AAAATTATATGATAAATTCAACTTGGCAACAGGAc                                                                                                          <  2:339653/135‑1 (MQ=11)
                           aTAGCTCAATGAATCTCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAAcct                                                                                                        <  2:87522/141‑2 (MQ=255)
                            tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                       <  1:194475/138‑1 (MQ=9)
                            gaaCTCAATGCAGATCTTAGATAGGAGCCAACAGCTACAGTGATAACATCCTTGTTAAAGGGTTTATGTGTGAAATAGGTCATACAGAAGACTCCGTTTTGTT‑AAAATTAGACTATAAATTCAACTTGGCAACAGAACCgc                                                                                                       >  2:11779/2‑140 (MQ=11)
                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGTACCAGAACCGtat                                                                                                     >  1:355051/2‑141 (MQ=255)
                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                     <  1:55524/140‑1 (MQ=12)
                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                     >  2:80198/2‑141 (MQ=12)
                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                     <  2:260222/140‑1 (MQ=12)
                                 cAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGtattat                                                                                                  >  1:344436/1‑141 (MQ=255)
                                   atgcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATGTTATAAATTCAACTTTGCAACAGAACCGtattttat                                                                                                >  1:431513/5‑137 (MQ=255)
                                    tgcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatg                                                                                               >  1:206287/4‑136 (MQ=255)
                                     gcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatg                                                                                               >  2:46179/3‑136 (MQ=11)
                                     gcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatga                                                                                              >  1:286473/3‑135 (MQ=255)
                                       atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATa                                                                                            <  1:5317/141‑1 (MQ=255)
                                        tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTTAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                           <  1:210698/141‑10 (MQ=11)
                                        tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatta                                                                                           >  1:366780/1‑127 (MQ=11)
                                         atCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtac                                                                                          >  1:155771/1‑131 (MQ=255)
                                           cTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacac                                                                                        <  2:170464/141‑13 (MQ=11)
                                           cTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAgaga                                                                                        >  1:437625/1‑141 (MQ=255)
                                            ttAGATAGTAGCGAACGGCGAGAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTGTGCAACAGAACCGtattttatgagtacact                                                                                       <  2:409748/141‑14 (MQ=11)
                                             tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                      <  1:308050/141‑15 (MQ=11)
                                             tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                      <  1:129192/141‑15 (MQ=11)
                                             tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATAGCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                      <  1:243131/141‑15 (MQ=11)
                                                aTAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTg                                                                                   >  1:428972/1‑141 (MQ=255)
                                                   gtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTa                                                                                >  2:146942/1‑141 (MQ=255)
                                                     agCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAAc                                                                              >  1:194300/1‑141 (MQ=255)
                                                     agCCAACGGCTACAGTGATAACAACCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAAc                                                                              >  2:398298/1‑141 (MQ=255)
                                                      gCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGTACCGTATTATGGAATAGAGATGTTGGTAACa                                                                             >  2:207505/1‑141 (MQ=255)
                                                        cgttggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACAtt                                                                           >  2:251960/5‑141 (MQ=255)
                                                         aaCGGCTACAGTGATAACATCCTTGTTAAATCGTGTATAGCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACAttt                                                                          >  1:448849/1‑141 (MQ=255)
                                                           cGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtat                                                                        >  2:155299/1‑141 (MQ=255)
                                                            ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTT‑ATTTTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtata                                                                       >  2:79414/1‑141 (MQ=18)
                                                               tACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAg                                                                    >  1:245196/1‑141 (MQ=255)
                                                                aCAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAgg                                                                   >  1:187579/1‑141 (MQ=255)
                                                                     gATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCAt                                                              <  2:142773/141‑1 (MQ=255)
                                                                          cATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATAc                                                         <  2:86266/141‑1 (MQ=255)
                                                                           aTCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACt                                                        >  1:342932/1‑141 (MQ=255)
                                                                           aTCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATGATACt                                                        >  2:370264/1‑141 (MQ=255)
                                                                             ccTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTa                                                      >  2:143967/1‑141 (MQ=255)
                                                                              cTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTaa                                                     <  2:347233/141‑1 (MQ=255)
                                                                               ttGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAg                                                    <  1:398298/141‑1 (MQ=255)
                                                                                 gTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGtt                                                  >  2:332940/1‑141 (MQ=255)
                                                                                 gTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGtt                                                  <  2:447634/141‑1 (MQ=255)
                                                                                   tAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTa                                                >  2:181424/1‑141 (MQ=255)
                                                                                        tGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTT‑TTTTTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTc                                           >  2:50617/1‑141 (MQ=37)
                                                                                                 cTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACa                                  >  2:261253/1‑141 (MQ=255)
                                                                                                  tGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAg                                 <  2:274089/141‑1 (MQ=255)
                                                                                                   gAAATAGTTCATACAGAAGACTCCTTTTTGTT‑TAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGa                                >  2:146815/1‑141 (MQ=255)
                                                                                                   gAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGa                                <  2:236106/141‑1 (MQ=255)
                                                                                                        aGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcac                           <  1:35125/141‑1 (MQ=255)
                                                                                                                   aagaCTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAAcc                >  2:95702/1‑141 (MQ=255)
                                                                                                                   aagaCTCCTTGATGTA‑AAAAGTATACTATAAATTCAACTTTGCAACAGAACCATATTATGGAATAGAAATATTGGTAACATGTATATAAGATCATTATACTTAAGTTTAATTTGGTTATTACACAACCACACATTACAAcc                >  2:95645/1‑141 (MQ=37)
                                                                                                                         ccTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCagaaga          <  1:340178/141‑1 (MQ=255)
                                                                                                                            ttttGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGaa       >  1:419430/1‑141 (MQ=255)
                                                                                                                                 tt‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTAt  >  1:362577/1‑141 (MQ=255)
                                                                                                                                             |                                                                                                                                 
TTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTT‑AAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTAT  >  CP000730/36441‑36710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A