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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,289,526 A→G K94K (AAA→AAG)  nrfB → nitrite reductase, formate‑dependent, penta‑heme cytochrome c

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,289,5260AG98.6% 249.2 / ‑4.5 72K94K (AAA→AAG) nrfBnitrite reductase, formate‑dependent, penta‑heme cytochrome c
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (35/36);  total (35/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01

AAACATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCGTT  >  NC_000913/4289431‑4289621
                                                                                               |                                                                                               
aaaCATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGAtg                                                                                             <  1:756765/100‑1 (MQ=255)
   cATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGa                                                                                          <  2:860022/100‑1 (MQ=255)
   cATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGa                                                                                          <  2:1228610/100‑1 (MQ=255)
     tGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATg                                                                                        <  2:1388568/100‑1 (MQ=255)
       cTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgc                                                                                       >  2:488782/1‑99 (MQ=255)
        ttCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATgcgc                                                                                     <  1:114063/100‑1 (MQ=255)
         tCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCt                                                                                    <  1:421873/100‑1 (MQ=255)
         tCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCt                                                                                    <  1:613932/100‑1 (MQ=255)
          ccGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGGCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCtt                                                                                   <  2:118516/100‑1 (MQ=255)
           cGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCttt                                                                                  >  1:58858/1‑100 (MQ=255)
           cGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCttt                                                                                  >  1:59980/1‑100 (MQ=255)
            gTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTa                                                                                 >  1:1239577/1‑100 (MQ=255)
              tATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAAc                                                                               <  2:1215719/100‑1 (MQ=255)
               aTCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACg                                                                              <  1:298189/100‑1 (MQ=255)
                 cAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAg                                                                            >  2:584198/1‑100 (MQ=255)
                  aaCCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGc                                                                           >  1:624428/1‑100 (MQ=255)
                   aCCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGcc                                                                          <  1:1021340/100‑1 (MQ=255)
                    cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                         >  1:396376/1‑100 (MQ=255)
                    cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                         <  2:1190969/100‑1 (MQ=255)
                    cccGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCg                                                                         >  1:1279676/1‑100 (MQ=255)
                       gAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATg                                                                      <  2:703962/100‑1 (MQ=255)
                           aaCAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGACGGGGAGAAGGATGTGATGCGCTTTAACGAGCCGATGTAc                                                                   >  2:556719/1‑99 (MQ=255)
                             cAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAg                                                                <  2:754705/100‑1 (MQ=255)
                               aaCTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGt                                                              >  1:609625/1‑100 (MQ=255)
                                  tGCCGGTCACCTGCACCAACTGGCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTgg                                                           <  2:390210/100‑1 (MQ=255)
                                   gCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTgg                                                           <  2:456898/99‑1 (MQ=255)
                                   gCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGga                                                          <  2:164217/100‑1 (MQ=255)
                                   gCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGga                                                          >  1:631450/1‑100 (MQ=255)
                                    ccGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgag                                                         >  1:176032/1‑100 (MQ=255)
                                    ccGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgag                                                         <  2:1092989/100‑1 (MQ=255)
                                     cGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgaga                                                        >  2:540696/1‑100 (MQ=255)
                                     cGGTCACCTGCACCAACTGTCACGGCCAGCCAGCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGgag                                                         <  2:1096043/99‑1 (MQ=255)
                                      ggTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGagag                                                       <  1:938037/100‑1 (MQ=255)
                                      ggTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGagag                                                       >  1:762611/1‑100 (MQ=255)
                                        tCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCa                                                     <  2:184510/100‑1 (MQ=255)
                                           ccTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGCGCCGATGTACAAGGTTGGAGAGCAGa                                                   >  2:1056916/1‑99 (MQ=255)
                                            cTGCAGCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAAc                                                 <  1:34346/100‑1 (MQ=255)
                                              gCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAg                                               >  1:19358/1‑100 (MQ=255)
                                                 ccAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGt                                            >  1:620167/1‑100 (MQ=255)
                                                   aaCTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTc                                           >  1:1033954/1‑99 (MQ=255)
                                                    aCTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTg                                         >  2:1399019/1‑100 (MQ=255)
                                                     cTGTCACGGCCTGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGt                                        <  2:198713/100‑1 (MQ=255)
                                                       gTCACGGCCAGCCATCACCGCAACCCCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGATCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTg                                         <  2:791709/97‑1 (MQ=255)
                                                       gTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTAt                                      >  2:99055/1‑100 (MQ=255)
                                                         cACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGt                                    >  2:869975/1‑100 (MQ=255)
                                                         cACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGt                                    >  1:1016385/1‑100 (MQ=255)
                                                           cGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTcc                                  <  2:931045/100‑1 (MQ=255)
                                                                 gccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCAt                            <  1:1412363/100‑1 (MQ=255)
                                                                  ccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATc                           <  1:1172609/100‑1 (MQ=255)
                                                                  ccaTCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATc                           <  1:1505055/100‑1 (MQ=255)
                                                                     tCACCGCAACACCGCTAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGc                        >  1:1240257/1‑100 (MQ=255)
                                                                     tCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGc                        <  2:788841/100‑1 (MQ=255)
                                                                     tCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGc                        <  2:540906/100‑1 (MQ=255)
                                                                     tCACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGc                        <  2:1197050/100‑1 (MQ=255)
                                                                      cACCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGcc                       >  2:708640/1‑100 (MQ=255)
                                                                       aCCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTg                         >  2:347292/1‑97 (MQ=255)
                                                                       aCCGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCg                      <  2:1521358/100‑1 (MQ=255)
                                                                        ccGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGCGCAGAACAGCGTCTGTATGTCCTGTCATCTGcc                       >  1:675536/1‑98 (MQ=255)
                                                                        ccGCAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCgg                     <  1:892368/100‑1 (MQ=255)
                                                                           cAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAAc                  >  2:843226/1‑100 (MQ=255)
                                                                           cAACACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAAc                  <  1:994191/100‑1 (MQ=255)
                                                                            aaCACCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACa                 >  2:449620/1‑100 (MQ=255)
                                                                             acacCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAg                <  1:496725/100‑1 (MQ=255)
                                                                              cacCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGt               >  1:1132729/1‑100 (MQ=255)
                                                                               acCGCGAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGtt              >  2:1459029/1‑100 (MQ=255)
                                                                                 cgcgAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGc            <  2:1139859/100‑1 (MQ=255)
                                                                                 cgcgAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGc            >  2:1106150/1‑100 (MQ=255)
                                                                                   cgAAGGGGTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCaa          >  1:768017/1‑100 (MQ=255)
                                                                                     aaGTGGTGAAGGATGTGATGCTCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCa           <  1:1319707/97‑1 (MQ=255)
                                                                                       ggggTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACATGGTTGGAGAGCAGAACAGCATCTGTATGTCCTGTCATCTGCCGGAACAGTTGCaaata       >  2:1510836/1‑97 (MQ=255)
                                                                                          gTGAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCGt   >  1:407031/1‑100 (MQ=255)
                                                                                            gAAGGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCGtt  >  2:408931/1‑99 (MQ=255)
                                                                                               |                                                                                               
AAACATGCTTCCGTTATCAACCCGAATAACAAACTGCCGGTCACCTGCACCAACTGTCACGGCCAGCCATCACCGCAACACCGCGAAGGGGTGAAAGATGTGATGCGCTTTAACGAGCCGATGTACAAGGTTGGAGAGCAGAACAGCGTCTGTATGTCCTGTCATCTGCCGGAACAGTTGCAAAAAGCGTT  >  NC_000913/4289431‑4289621

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A