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 F58 I0 R1 54 56.9 1222162 95.8% 1170831 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,413 C→T 8.1% V47I (GTC→ATC)  tpn ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,4130CT 8.1% 153.1 / 4.6 63V47I (GTC→ATC) tpnIS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (31/25);  new base T (3/2);  total (35/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

GCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCA  >  CP000730/36277‑36550
                                                                                                                                        |                                                                                                                                         
gCACGTTATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTCTACCGtt                                                                                                                                       <  1:216200/141‑1 (MQ=255)
   cGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTTaa                                                                                                                                    >  1:68961/1‑141 (MQ=255)
   cGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGaa                                                                                                                                    >  1:96042/1‑141 (MQ=40)
     atatAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAatg                                                                                                                                  <  2:379554/141‑1 (MQ=40)
         aattAGCTCCATTTTCCTCTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAAtgatga                                                                                                                              <  1:483970/138‑1 (MQ=255)
          aaTAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGATATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGaa                                                                                                                             >  1:541872/1‑141 (MQ=11)
          aaTACCGCCATTTTCCTTTTATTTTGATGTACGTCGCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATCAGAAAAAACACTGGGGCATATTCTTGAACCCAACGGTAGACCGTTCAATGATGaa                                                                                                                             <  2:585779/141‑1 (MQ=11)
             aGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCACCGGTAGACCGTTGGATGATGAACGt                                                                                                                          >  1:544553/1‑141 (MQ=255)
             aGCTCCATTTTCCTGTGATTTTGATGTACGCCTCATCAATACGCCATTTGTAATAAGCGTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATGGAGGAACATTCTTCAACCCAACCGACAACCCTGGGATGATGAACGt                                                                                                                          >  2:559397/1‑141 (MQ=11)
               cTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGttt                                                                                                                        >  1:392754/1‑141 (MQ=255)
                  cATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTaca                                                                                                                     >  1:481481/1‑141 (MQ=40)
                   aTTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTTATACAACATTGGGGCATATTCTTGAACCCAACGGTAGACCGCTGCATGGTCACCGtttttac                                                                                                                    >  2:247622/1‑137 (MQ=14)
                   aTTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTacac                                                                                                                    >  1:525587/1‑141 (MQ=40)
                    ttttCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcacc                                                                                                                   <  1:38464/141‑1 (MQ=40)
                        ccTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGt                                                                                                               <  2:96042/141‑1 (MQ=40)
                        ccTTTTATTTTGACAAACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGTACGTTTACACCACGt                                                                                                               <  2:467641/141‑1 (MQ=11)
                          ttttATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTc                                                                                                             <  1:455602/141‑1 (MQ=255)
                           tttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTcc                                                                                                            >  1:32683/1‑141 (MQ=40)
                            ttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc                                                                                                           <  1:174817/141‑1 (MQ=40)
                            ttATTGTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc                                                                                                           <  1:300952/141‑1 (MQ=255)
                              tttttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTTTGGTGTGTCTGCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCtt                                                                                                         <  1:17232/140‑1 (MQ=14)
                              aTTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCtt                                                                                                         <  2:461496/141‑1 (MQ=39)
                                   gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGGAGACCGTTGAATGATGAACGTTTAAACAACGTGCCCTTGatat                                                                                                    >  1:507434/1‑141 (MQ=14)
                                   gATGTACGTCTCATCAATACGCAATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAAATGGGAAATATAATTACACCCAACGGTAACACGTTGAATGATGAACGTTTACACCACGTTCCCTTAatat                                                                                                    >  1:580722/1‑141 (MQ=14)
                                      gTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAGATTTGATACAAAATTGGGGAATATTCGTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTACCTTAATATTTc                                                                                                 >  2:336583/1‑141 (MQ=255)
                                          ttctcATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGat                                                                                             <  2:312879/140‑1 (MQ=40)
                                           tctcATCAATACGCCATTTGTAATAAGTTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGata                                                                                            <  2:515355/141‑1 (MQ=255)
                                            ctcATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatat                                                                                           >  1:251282/1‑141 (MQ=40)
                                                tcaATACGCCATTTGTAATCAAAGATTTGATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAATGGTAGACCGTTGAATGATGAACGTTTACACAACGTTCCCTTAATATTTCAGATATATCa                                                                                       >  2:281828/1‑141 (MQ=11)
                                                tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCa                                                                                       <  1:572591/141‑1 (MQ=40)
                                                   aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  1:486745/141‑1 (MQ=39)
                                                   aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  1:447603/141‑1 (MQ=39)
                                                   aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAAGTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  2:366754/141‑1 (MQ=255)
                                                      cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGTCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATag                                                                                 >  2:177700/1‑140 (MQ=255)
                                                        ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAAGGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                               >  2:84331/1‑141 (MQ=255)
                                                                 ataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGtata                                                                      <  1:191739/141‑1 (MQ=40)
                                                                    aGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCt                                                                   <  2:408153/141‑1 (MQ=38)
                                                                    aGCTTGTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTCCCCTTAATATTTCAGATATATCACGATAACTCAATGTATctct                                                                   >  2:86107/1‑141 (MQ=255)
                                                                      cTTTTTTAGGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTa                                                                 <  1:426853/141‑1 (MQ=37)
                                                                       ttttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAg                                                                >  1:356141/1‑141 (MQ=35)
                                                                        tttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGa                                                               >  2:553933/1‑141 (MQ=35)
                                                                         ttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACAATAACTCAATGTATATCTTAGaa                                                              >  2:116333/1‑140 (MQ=25)
                                                                                atttttCTTCCACAGTTGAAACCAAACCGGGGCATATTCTTGAACCCAACGGTAGGCCGTTGAATGATGAACGTGTACACCACGTTCCCTTAATGTTTCAGATATATCACCATACCTCAATGTATATCTAAGATAATGGcc                                                       >  2:37945/2‑141 (MQ=11)
                                                                                   tttCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCACTGTATATCTTAGATAGTAGCCAAc                                                    >  1:241858/1‑141 (MQ=25)
                                                                                     tcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGAAGACCGTTGGATGATGAACGTGTACACCACGTTCCCTTACTATTTCAGATATACCACGCTAACCCCGTGTCTATCTTAGAtagtcaacgtagc                                                  >  1:283545/1‑132 (MQ=11)
                                                                                      cttcCAAATTGGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGc                                                 <  1:576262/141‑1 (MQ=25)
                                                                                       ttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGGTACCTCAATGTATATCTTAGCTAGTAGACAACggat                                                >  2:499882/1‑139 (MQ=255)
                                                                                                         aTTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTg                              <  2:496123/141‑1 (MQ=32)
                                                                                                          ttGGGGCATATTCCTGATCCCAACGGTAGACCGGTGAATGATGAACGTTTAAACCACTTTCTCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGt                             <  2:523551/141‑1 (MQ=11)
                                                                                                            ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                           >  2:37356/1‑141 (MQ=32)
                                                                                                            ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                           >  1:562150/1‑141 (MQ=32)
                                                                                                             gggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaa                          >  1:572755/1‑141 (MQ=32)
                                                                                                                    ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGttt                   <  1:332576/141‑1 (MQ=32)
                                                                                                                       ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATATTAGATAGTAACCAACGGCTACAGTGCTACAATCCTTGTTAAATTGTTttta                >  2:323642/1‑141 (MQ=11)
                                                                                                                        tGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCGGATATATCACGATAACTCTATGTATATCTTGGTTACGAGCCAACGGCTACAGTGATAACCACGTGGTTCAATCGTTTatat               >  1:536746/1‑141 (MQ=11)
                                                                                                                             ccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaa          >  2:15157/1‑141 (MQ=32)
                                                                                                                              cAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa         >  1:392396/1‑141 (MQ=32)
                                                                                                                               aaCGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACCTCCTTGTTAAATTGTTTATATCTGAAAt        >  2:121024/1‑141 (MQ=17)
                                                                                                                               aaCGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAAt        >  2:120974/1‑141 (MQ=32)
                                                                                                                                   gTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:32683/141‑1 (MQ=32)
                                                                                                                                   gTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:142263/141‑1 (MQ=32)
                                                                                                                                   gTAGAACGTTGAATGATGAACGTTTACCCCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:380277/141‑1 (MQ=17)
                                                                                                                                     ctaCCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa  >  1:172451/3‑141 (MQ=17)
                                                                                                                                        |                                                                                                                                         
GCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCA  >  CP000730/36277‑36550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A