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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 835,342 C→T 43.6% H20H (CAC→CAT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3420CT43.6% 55.7 / 147.4 126H20H (CAC→CAT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (25/46);  new base T (21/34);  total (46/80)
Fisher's exact test for biased strand distribution p-value = 8.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

Only 100 of 133 total aligned reads displayed.

GAGAGCGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACG  >  minE/835272‑835412
                                                                      |                                                                      
gagaGCGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCcac                                                                        <  1:3211809/71‑1 (MQ=255)
   agCGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACAcc                                                                     <  1:104920/71‑1 (MQ=255)
      aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                                  <  1:2601292/69‑1 (MQ=255)
      aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                                  <  1:892720/69‑1 (MQ=255)
       tAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt                                                                 <  1:829840/71‑1 (MQ=255)
       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGATTAACCTCGAGAAATGTATCGGCTGCCATACCTGtt                                                                 <  1:515880/70‑1 (MQ=255)
         aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                                               >  1:2178191/1‑70 (MQ=255)
            tGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                                                <  1:2007373/67‑1 (MQ=255)
              aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTAc                                                          >  1:1753273/1‑71 (MQ=255)
              aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                                           <  1:2111745/70‑1 (MQ=255)
               aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc                                                         >  1:3033300/1‑71 (MQ=255)
                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                                                <  1:643041/63‑1 (MQ=255)
                aaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                                        <  1:3422085/71‑1 (MQ=255)
                 aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAg                                                              >  1:5531578/1‑64 (MQ=255)
                  tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGtg                                                            <  1:2521365/63‑2 (MQ=255)
                  tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                                        >  1:2955088/3‑69 (MQ=255)
                   ccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTg                                                       >  1:4929890/2‑69 (MQ=255)
                     gTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                                   <  1:39445/71‑1 (MQ=255)
                     gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                                    <  1:4627365/70‑1 (MQ=255)
                     gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                                    <  1:3824596/70‑1 (MQ=255)
                      ttCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                                 <  1:1244187/56‑1 (MQ=255)
                      ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTTTaaaa                                                  <  1:1391440/71‑1 (MQ=255)
                      ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaaa                                                  <  1:823694/71‑1 (MQ=255)
                      ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaa                                                   <  1:2080557/70‑1 (MQ=255)
                        cacaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAAc                                                >  1:2548851/1‑71 (MQ=255)
                           aaGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaaa                                                  >  1:5685662/1‑66 (MQ=255)
                              tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                                          <  1:5621635/71‑1 (MQ=255)
                              tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                                           <  1:4548543/70‑1 (MQ=255)
                                   aTGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGAccg                                      <  1:401755/70‑2 (MQ=255)
                                   aTGGTGCTGAATCTCTATAAGTGCATCGGCTGCCACAcc                                                                     <  1:1000773/39‑1 (MQ=255)
                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                                 <  1:1798066/42‑1 (MQ=255)
                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                                 <  1:3032749/42‑1 (MQ=255)
                                    tGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                                                <  1:4865397/43‑1 (MQ=255)
                                      gTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                                           >  1:4608998/1‑62 (MQ=255)
                                      gTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCg                                  <  1:696788/71‑1 (MQ=255)
                                        gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                                     >  1:921225/1‑50 (MQ=255)
                                        gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                                     >  1:2454457/1‑50 (MQ=255)
                                        gCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTACCTGTaa                                                    <  1:757831/51‑1 (MQ=255)
                                        gCTGAATCTCGATAAGTGCATCGGCTGCCACAGCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                 >  1:875915/1‑70 (MQ=255)
                                        gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                 >  1:4773351/1‑70 (MQ=255)
                                        gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                 >  1:4406792/1‑70 (MQ=255)
                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                                 >  1:4223772/1‑69 (MQ=255)
                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                >  1:1232917/1‑70 (MQ=255)
                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                <  1:4804319/70‑1 (MQ=255)
                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGa                               <  1:2550486/71‑1 (MQ=255)
                                            aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                            >  1:5108994/4‑71 (MQ=255)
                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                >  1:290336/1‑51 (MQ=255)
                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                >  1:557873/1‑51 (MQ=255)
                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                >  1:2485647/1‑51 (MQ=255)
                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                              <  1:1816674/69‑1 (MQ=255)
                                             acctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg                            <  1:1544852/68‑1 (MQ=255)
                                             aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTTAAGGc                           <  1:2791370/71‑1 (MQ=255)
                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                                             <  1:2429816/36‑1 (MQ=255)
                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCt                                                        >  1:1289996/1‑41 (MQ=255)
                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                              <  1:3492849/51‑1 (MQ=255)
                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                              <  1:4109947/51‑1 (MQ=255)
                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                                              <  1:2729899/51‑1 (MQ=255)
                                              cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca                          <  1:3393405/70‑2 (MQ=255)
                                              cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca                          <  1:1450542/70‑2 (MQ=255)
                                                tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTgg                                          >  1:511548/1‑53 (MQ=255)
                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg                             >  1:4838527/1‑66 (MQ=255)
                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                           <  1:1188328/68‑1 (MQ=255)
                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc                           <  1:4446910/68‑1 (MQ=255)
                                                 cGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                                           >  1:4888898/1‑51 (MQ=255)
                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                              >  1:225986/1‑63 (MQ=255)
                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                       <  1:757757/70‑1 (MQ=255)
                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                       >  1:5387749/1‑70 (MQ=255)
                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg                       <  1:2055536/70‑1 (MQ=255)
                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGCACCAGCCGTGAAGGCGTgg                       <  1:4789397/70‑1 (MQ=255)
                                                   aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                <  1:1283786/44‑1 (MQ=255)
                                                   aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                <  1:2326283/44‑1 (MQ=255)
                                                   aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                                <  1:3557967/44‑1 (MQ=255)
                                                    tAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACAAGCCGTGAAGGCGTGGAat                    <  1:5430758/71‑1 (MQ=255)
                                                      aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata                   <  1:5479613/70‑1 (MQ=255)
                                                       gTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg                 <  1:1222241/71‑1 (MQ=255)
                                                        tGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGc                <  1:2175775/71‑1 (MQ=255)
                                                         gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                              >  1:1063941/3‑40 (MQ=25)
                                                         gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                              >  1:5276277/3‑40 (MQ=25)
                                                         gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                              >  1:2341640/3‑40 (MQ=25)
                                                         gtaTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGt                                              >  1:4808949/3‑40 (MQ=25)
                                                          taTCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGcat              >  1:4991255/2‑69 (MQ=255)
                                                           aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg             <  1:4955137/71‑1 (MQ=255)
                                                           aTCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg             <  1:3262564/71‑1 (MQ=255)
                                                            tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                                <  1:3297691/51‑1 (MQ=255)
                                                            tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTgg            <  1:285264/71‑1 (MQ=255)
                                                            tCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTg             >  1:3219286/1‑70 (MQ=255)
                                                              ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGaa                              >  1:3579997/1‑51 (MQ=255)
                                                              ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGtt          <  1:1970209/71‑1 (MQ=255)
                                                              ggCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGt           <  1:2100921/70‑1 (MQ=255)
                                                              ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa                              >  1:2987253/1‑51 (MQ=255)
                                                              ggCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGt           >  1:2009209/1‑70 (MQ=255)
                                                                cTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca        <  1:1467275/71‑1 (MQ=255)
                                                                cTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTca        <  1:4868144/71‑1 (MQ=255)
                                                                   ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaaca     <  1:2643060/71‑1 (MQ=255)
                                                                   ccATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGCATGGAGTACGCATGGTTtaaca     <  1:814686/71‑1 (MQ=255)
                                                                   ccACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaac      <  1:471589/70‑1 (MQ=255)
                                                                    cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa    <  1:2951129/71‑1 (MQ=255)
                                                                    cacaCCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTcaacaa    <  1:3044269/71‑1 (MQ=255)
                                                                      cacCTGTTCAGTTACCTGTAAAAACGTCTGGCCCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg  <  1:4458463/71‑1 (MQ=255)
                                                                      cacCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACg  >  1:4128877/1‑71 (MQ=255)
                                                                      |                                                                      
GAGAGCGTAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATGCGTGGTTCAACAACG  >  minE/835272‑835412

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