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 835,324 T→C 40.8% D14D (GAT→GAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3240TC40.8% 84.5 / 158.0 146D14D (GAT→GAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (40/46);  new base C (28/31);  total (68/78)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 151 total aligned reads displayed.

GGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAAT  >  minE/835254‑835394
                                                                       |                                                                      
ggCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                                                        <  1:4381332/71‑1 (MQ=255)
 gCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                                                        <  1:4920049/70‑1 (MQ=255)
   aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                                                        >  1:178519/1‑68 (MQ=255)
   aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:4002944/1‑71 (MQ=255)
   aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:4613436/1‑71 (MQ=255)
   aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGGGCTGAATCTCGATaa                                                                      <  1:5613257/70‑1 (MQ=255)
    aTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:385532/1‑70 (MQ=255)
       aCCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                 >  1:233830/1‑71 (MQ=255)
        tcAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                                >  1:3005167/2‑71 (MQ=255)
        tcAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                                >  1:2954352/2‑71 (MQ=255)
        ccAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                 <  1:3122629/70‑1 (MQ=255)
         cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                               >  1:4734300/1‑71 (MQ=255)
         cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                               >  1:2118422/1‑71 (MQ=255)
         cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                               >  1:556670/1‑71 (MQ=255)
          aGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCg                                                              >  1:1446184/1‑71 (MQ=255)
            gTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                                                        <  1:4453539/59‑1 (MQ=255)
              aCAGGAGAGCG‑TAAAATGAGAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTg                                                          >  1:2227744/1‑71 (MQ=255)
                     agCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACAcc                                                   <  1:104920/71‑1 (MQ=255)
                         aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                <  1:2601292/69‑1 (MQ=255)
                          tAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt                                               <  1:829840/71‑1 (MQ=255)
                          aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGc                                                         >  1:1924013/2‑61 (MQ=255)
                          aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGc                                                         >  1:124944/2‑61 (MQ=255)
                          aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGATTAACCTCGAGAAATGTATCGGCTGCCATACCTGtt                                               <  1:515880/70‑1 (MQ=255)
                           aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                              >  1:2363345/1‑71 (MQ=255)
                            aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATa                                                                       <  1:2027004/45‑1 (MQ=255)
                            aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGt                                                                    <  1:3425474/48‑1 (MQ=255)
                            aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGt                                                                    <  1:4634673/48‑1 (MQ=255)
                            aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt                                               >  1:1677326/1‑69 (MQ=255)
                            aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                              <  1:4398764/70‑1 (MQ=255)
                            aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                             >  1:2178191/1‑70 (MQ=255)
                             aaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATgt                                                                  <  1:1707439/49‑2 (MQ=255)
                               tGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                              <  1:2007373/67‑1 (MQ=255)
                               tGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATg                                                                   <  1:3807655/46‑1 (MQ=255)
                               tGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATg                                                                   <  1:1345615/46‑1 (MQ=255)
                                 aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                         <  1:2111745/70‑1 (MQ=255)
                                 aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc                                        >  1:2988737/1‑71 (MQ=255)
                                  aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc                                       >  1:3033300/1‑71 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:844935/1‑40 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:31596/1‑40 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:4641487/1‑40 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                     >  1:1649166/1‑40 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                              <  1:643041/63‑1 (MQ=255)
                                   aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAcc                                       <  1:5463800/70‑1 (MQ=255)
                                   aaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                      <  1:3422085/71‑1 (MQ=255)
                                    aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                                >  1:1975393/1‑44 (MQ=255)
                                    aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                                >  1:4538003/1‑44 (MQ=255)
                                    aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                                >  1:2679041/1‑44 (MQ=255)
                                     ttCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGt                                    <  1:1202460/71‑1 (MQ=255)
                                     tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGtg                                          <  1:2521365/63‑2 (MQ=255)
                                     tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                      >  1:2955088/3‑69 (MQ=255)
                                      ccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTg                                     >  1:4929890/2‑69 (MQ=255)
                                        gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                  <  1:3824596/70‑1 (MQ=255)
                                        gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                  <  1:2735648/70‑1 (MQ=255)
                                         ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaaa                                <  1:823694/71‑1 (MQ=255)
                                          tCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGc                                                         <  1:2813408/45‑1 (MQ=255)
                                           cacaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCca                                                       >  1:5225096/1‑46 (MQ=255)
                                           cacaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGc                                                            >  1:5569008/1‑41 (MQ=255)
                                            acaAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACg                             >  1:3183088/1‑71 (MQ=255)
                                                 tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                        <  1:5621635/71‑1 (MQ=255)
                                                 tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                        <  1:3266844/71‑1 (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)
                                                       tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                              <  1:2512733/43‑1 (MQ=255)
                                                       tGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                              <  1:4865397/43‑1 (MQ=255)
                                                         gTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                         >  1:4608998/1‑62 (MQ=255)
                                                           gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                   >  1:2454457/1‑50 (MQ=255)
                                                           gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                   >  1:921225/1‑50 (MQ=255)
                                                           gCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTACCTGTaa                                  <  1:757831/51‑1 (MQ=255)
                                                           gCTGAATCTCGATAAGTGCATCGGCTGCCACAGCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt               >  1:875915/1‑70 (MQ=255)
                                                           gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt               >  1:4773351/1‑70 (MQ=255)
                                                            cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt               >  1:4223772/1‑69 (MQ=255)
                                                            cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg              <  1:4804319/70‑1 (MQ=255)
                                                            cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg              >  1:1232917/1‑70 (MQ=255)
                                                            cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGa             <  1:2550486/71‑1 (MQ=255)
                                                               aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg          >  1:5108994/4‑71 (MQ=255)
                                                               aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                              >  1:290336/1‑51 (MQ=255)
                                                                acctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg          <  1:1544852/68‑1 (MQ=255)
                                                                 tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                           <  1:2429816/36‑1 (MQ=255)
                                                                 tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCt                                      >  1:1289996/1‑41 (MQ=255)
                                                                 tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                            <  1:4109947/51‑1 (MQ=255)
                                                                 tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                            <  1:3492849/51‑1 (MQ=255)
                                                                 tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                            <  1:2729899/51‑1 (MQ=255)
                                                                 cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca        <  1:1450542/70‑2 (MQ=255)
                                                                  ctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGcat       <  1:3733652/71‑3 (MQ=255)
                                                                   tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                         >  1:690910/1‑36 (MQ=255)
                                                                   tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTgg                        >  1:511548/1‑53 (MQ=255)
                                                                   tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                 <  1:1253319/44‑1 (MQ=16)
                                                                   tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg           >  1:4838527/1‑66 (MQ=255)
                                                                   tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc         <  1:1833308/68‑1 (MQ=255)
                                                                   tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc         <  1:4446910/68‑1 (MQ=255)
                                                                    cGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                         >  1:4888898/1‑51 (MQ=255)
                                                                     gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa            >  1:225986/1‑63 (MQ=255)
                                                                     gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg     <  1:2055536/70‑1 (MQ=255)
                                                                     gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg     <  1:757757/70‑1 (MQ=255)
                                                                     gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg     >  1:2555624/1‑70 (MQ=255)
                                                                      aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                              <  1:2184372/44‑1 (MQ=255)
                                                                      aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                              <  1:3557967/44‑1 (MQ=255)
                                                                       tAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACAAGCCGTGAAGGCGTGGAat  <  1:5430758/71‑1 (MQ=255)
                                                                       |                                                                      
GGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAAT  >  minE/835254‑835394

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A