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
A20 F48 I1 R1 52 61.9 2103308 98.8% 2078068 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 711,559 C→A intergenic (‑94/+46) fldA ← / ← ybfE flavodoxin 1/LexA‑regulated protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913711,5590CA96.5% 199.0 / 1.0 58intergenic (‑94/+46)fldA/ybfEflavodoxin 1/LexA‑regulated protein
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (23/33);  total (24/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.92e-01

TTACCGGTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATATTGCGCGA  >  NC_000913/711425‑711688
                                                                                                                                      |                                                                                                                                 
ttACCGGTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCaa                                                                                                                              <  1:181546/140‑1 (MQ=255)
ttACCGGTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCaa                                                                                                                              <  2:325178/140‑1 (MQ=255)
ttACCGGTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCaa                                                                                                                              <  2:190999/140‑1 (MQ=255)
     ggTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAg                                                                                                                         <  2:92798/140‑1 (MQ=255)
     ggTGTCGCTGCCGAAAAAGATACCAGTGATAGCCATGAGTGAAATAGCCTCTCGAAACTTATTGAAATGGGGGTGGAAAATTGCACCCGGATAAAGGCAATCATAGCAGAACCGGCAGTCTTGCGGAATAAGCAAACGAg                                                                                                                         <  2:219518/140‑1 (MQ=255)
       tgtCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCa                                                                                                                       <  1:520811/140‑1 (MQ=255)
       tgtCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCa                                                                                                                       <  1:514132/140‑1 (MQ=255)
            cTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACt                                                                                                                  <  1:778183/140‑1 (MQ=255)
             tGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTg                                                                                                                 <  2:653931/140‑1 (MQ=255)
               ccGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGca                                                                                                               <  1:172174/140‑1 (MQ=255)
                 gAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGcaca                                                                                                             <  2:150090/140‑1 (MQ=255)
                 gAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGcaca                                                                                                             <  1:224442/140‑1 (MQ=255)
                 gAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGcaca                                                                                                             <  1:693144/140‑1 (MQ=255)
                 gAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGcaca                                                                                                             <  1:645585/140‑1 (MQ=255)
                      aGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACtgtg                                                                                                        <  2:913607/140‑1 (MQ=255)
                      aGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACtgtg                                                                                                        >  2:539728/1‑140 (MQ=255)
                      aGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACtgtg                                                                                                        <  1:539728/140‑1 (MQ=255)
                         tGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTa                                                                                                     >  1:407355/1‑140 (MQ=255)
                         tGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTa                                                                                                     >  2:312359/1‑140 (MQ=255)
                                   aGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTg                                                                                           <  2:593593/140‑1 (MQ=255)
                                        tGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAAt                                                                                      >  2:242441/1‑140 (MQ=255)
                                         gAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAAtt                                                                                     >  1:653420/1‑140 (MQ=255)
                                         gAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAAtt                                                                                     >  2:82210/1‑140 (MQ=255)
                                              aaaTAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAAc                                                                                <  1:737939/140‑1 (MQ=255)
                                               aaTAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACg                                                                               >  1:592548/1‑140 (MQ=255)
                                                    ccTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGcc                                                                          >  1:186873/1‑140 (MQ=255)
                                                    ccTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGcc                                                                          >  2:455760/1‑140 (MQ=255)
                                                    ccTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGcc                                                                          >  1:1030434/1‑140 (MQ=255)
                                                    ccTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGcc                                                                          >  1:336405/1‑140 (MQ=255)
                                                      tctTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACg                                                                               <  1:597492/133‑1 (MQ=255)
                                                      tctTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACg                                                                               >  2:597492/1‑133 (MQ=255)
                                                       ctTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCtt                                                                       >  2:578681/1‑139 (MQ=255)
                                                         tGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGAc                                                                     >  1:641551/1‑140 (MQ=255)
                                                         tGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGAc                                                                     >  1:28610/1‑140 (MQ=255)
                                                             aCTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACg                                                                 <  1:82210/140‑1 (MQ=255)
                                                                  ttGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                                            >  1:50472/1‑140 (MQ=255)
                                                                  ttGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                                            >  2:671963/1‑140 (MQ=255)
                                                                  ttGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAgcg                                                            >  2:539414/1‑140 (MQ=255)
                                                                          ggggTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGt                                                    >  1:901351/1‑140 (MQ=255)
                                                                            ggTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtg                                                  <  2:336405/140‑1 (MQ=255)
                                                                              tGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgct                                                <  2:592548/140‑1 (MQ=255)
                                                                              tGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgct                                                <  2:28610/140‑1 (MQ=255)
                                                                              tGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgct                                                <  1:177043/140‑1 (MQ=255)
                                                                                gAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTtgctgc                                              <  1:578681/140‑1 (MQ=255)
                                                                                  aaaTTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCAt                                            <  1:384188/140‑1 (MQ=255)
                                                                                      tGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCAAGTTGCTGCGTTAAc                                        <  1:242441/140‑1 (MQ=255)
                                                                                       gCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACa                                       <  1:469457/140‑1 (MQ=255)
                                                                                       gCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACa                                       <  2:1030434/140‑1 (MQ=255)
                                                                                         ccACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACAtc                                     <  2:641551/140‑1 (MQ=255)
                                                                                                        aTCATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCg                      >  2:130506/1‑140 (MQ=255)
                                                                                                          cATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCt                    <  1:539414/140‑1 (MQ=255)
                                                                                                          cATAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCt                    <  1:312359/140‑1 (MQ=255)
                                                                                                          aaTAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCt                    <  2:407355/139‑1 (MQ=255)
                                                                                                           aTAGCAGAACAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTa                   <  2:901351/140‑1 (MQ=255)
                                                                                                                  aaCAGGCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCa            <  2:186873/140‑1 (MQ=255)
                                                                                                                       gCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATAttt       >  2:596417/1‑139 (MQ=255)
                                                                                                                       gCAGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATATTg       >  1:947530/1‑140 (MQ=255)
                                                                                                                         aGTCTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATATTgcg     >  1:960580/1‑140 (MQ=255)
                                                                                                                            cTTGCGGAATAAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATATTGCGCGa  >  2:85582/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                 
TTACCGGTGTCGCTGCCGAAAAAGATGCCAGTGATAGCCATGAGTGAAATAACCTCTTGAAACTTATTGAAATGGGGGTGGAAAATTGCCCACGGATAAAGGCAATCATAGCAGAACAGGCAGTCTTGCGGAATCAGCAAACGAGCAGGACTGCACACTGTGCTACATGAAAGTGGAAATTTAAACGATGCCCTGACTACGCAGCGCCGCCAGTTGCTGCATTAACATCTCTTCGATCAGTTCGCTACGGCTCATATTGCGCGA  >  NC_000913/711425‑711688

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A