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 835,211 T→C 23.7% V1223V (GTT→GTC) ‡ narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2110TC23.7% 198.3 / 62.5 114V1223V (GTT→GTC) ‡narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (40/47);  new base C (16/11);  total (56/58)
Fisher's exact test for biased strand distribution p-value = 2.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 129 total aligned reads displayed.

CGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG  >  minE/835142‑835278
                                                                     |                                                                   
cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:809850/71‑1 (MQ=255)
cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:3619986/71‑1 (MQ=255)
   cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  >  1:3173179/1‑70 (MQ=255)
    tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt                                                                >  1:235901/1‑71 (MQ=255)
        cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                                            <  1:140015/71‑1 (MQ=255)
         ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                                                 >  1:4510044/1‑65 (MQ=255)
         ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                                                                 >  1:4361515/1‑65 (MQ=255)
                 cATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                                   <  1:3865259/71‑1 (MQ=255)
                 cATACGGCTTTAACTACTATGGCACCGTAGGTCCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag                                                   <  1:3211259/71‑1 (MQ=255)
                   tACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:4254182/52‑1 (MQ=255)
                    ggggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAc                                                >  1:4667421/3‑71 (MQ=255)
                    aCGGCTATAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaagaa                                                 >  1:730620/1‑70 (MQ=255)
                     cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  >  1:5170029/1‑52 (MQ=255)
                     cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                                                                  >  1:4306227/1‑52 (MQ=255)
                     cGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                               >  1:5614683/1‑71 (MQ=255)
                      ggCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcgt                                              <  1:2579900/71‑3 (MQ=255)
                       gCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             <  1:2893467/71‑1 (MQ=255)
                        cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAtt                                             >  1:3862488/1‑70 (MQ=255)
                         tttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGtt                                             <  1:2956660/69‑1 (MQ=255)
                            aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACt                                         <  1:3100500/70‑1 (MQ=255)
                            aaCTACTACGGGACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                                                 >  1:5171552/1‑62 (MQ=255)
                            aaCTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATgaagaa                                                 >  1:3456343/1‑62 (MQ=255)
                             actactATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg                                                                    <  1:1108825/42‑1 (MQ=255)
                             actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACAt                                              >  1:3442705/1‑64 (MQ=255)
                             actactATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                       <  1:4961804/71‑1 (MQ=255)
                              ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTgg                                       <  1:4001945/70‑1 (MQ=255)
                              ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      <  1:2812972/71‑1 (MQ=255)
                              ctactaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      <  1:105446/71‑1 (MQ=255)
                              ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                      <  1:3275169/71‑2 (MQ=255)
                               tactaTGGCACCGTAGGTTCTAACCGCGATGAGTTtgttgt                                                                   <  1:4172156/41‑1 (MQ=255)
                                 ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      >  1:5368718/1‑68 (MQ=255)
                                 ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                      >  1:4961987/1‑68 (MQ=255)
                                   acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                 >  1:256060/3‑71 (MQ=255)
                                   acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAACAACGTTAACTGGCTGGAt                                 >  1:359637/3‑71 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                                    >  1:1035745/1‑51 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaa                                                    >  1:3205365/1‑51 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                               <  1:5095584/56‑1 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                  <  1:1103606/69‑1 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                  <  1:5171278/69‑1 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                  <  1:1230388/69‑1 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                  <  1:1782557/69‑1 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                >  1:1344664/1‑71 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                >  1:1580240/1‑71 (MQ=255)
                                    tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                >  1:5242741/1‑71 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAAcg                                               >  1:1312757/2‑55 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                                           >  1:5650863/2‑58 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGttaa                                           >  1:2452135/2‑58 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                 <  1:1590219/69‑1 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                 <  1:3390824/69‑1 (MQ=255)
                                    cggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                 <  1:4956914/69‑1 (MQ=255)
                                     ggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                               <  1:5684417/71‑2 (MQ=255)
                                      gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                              >  1:3678124/1‑69 (MQ=255)
                                      gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                              >  1:227615/1‑69 (MQ=255)
                                      gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                              >  1:2619988/1‑69 (MQ=255)
                                      gCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATga                               >  1:5190126/1‑69 (MQ=255)
                                      gCACCGTCGGATCGAACCGCGATGACTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                              <  1:733046/71‑3 (MQ=255)
                                      gCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATgg                               <  1:5209487/70‑1 (MQ=255)
                                       cACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATgat                              >  1:3810990/1‑68 (MQ=255)
                                       cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGc                                                              <  1:1586383/38‑1 (MQ=255)
                                       cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGTAGAACATTGACTGGTTAGATGGCg                             <  1:2297451/71‑1 (MQ=255)
                                       cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                   >  1:5296291/1‑65 (MQ=255)
                                       cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                   >  1:1898385/1‑65 (MQ=255)
                                       cACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                             <  1:2292372/71‑1 (MQ=255)
                                         ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCg                             >  1:2935844/1‑69 (MQ=255)
                                          cGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                       <  1:3136321/58‑1 (MQ=255)
                                          cGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGt                                                            <  1:2258041/37‑1 (MQ=255)
                                           gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGa                                                        >  1:4806926/1‑40 (MQ=255)
                                           gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGGAGAACATTGACTGGTTa                                    >  1:2039359/1‑60 (MQ=255)
                                           gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    >  1:1116169/1‑60 (MQ=255)
                                           gTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAgg                         >  1:932341/1‑71 (MQ=255)
                                            tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACa                                               >  1:3197425/1‑48 (MQ=255)
                                               gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:5485123/56‑1 (MQ=255)
                                               gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     <  1:4239680/71‑1 (MQ=255)
                                               gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                     <  1:959522/71‑1 (MQ=255)
                                                ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                            <  1:3286952/63‑1 (MQ=255)
                                                ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                            <  1:1123275/63‑1 (MQ=255)
                                                 tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                  >  1:4039788/1‑56 (MQ=255)
                                                 tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                              <  1:4522556/60‑1 (MQ=255)
                                                 tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGc                              <  1:1346366/60‑1 (MQ=255)
                                                 tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGa                   >  1:785147/1‑71 (MQ=255)
                                                  cTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  >  1:340032/1‑71 (MQ=255)
                                                   tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:4870463/52‑1 (MQ=255)
                                                   tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                    <  1:628252/52‑1 (MQ=255)
                                                   tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  >  1:4231039/1‑70 (MQ=255)
                                                    aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  >  1:5509325/1‑69 (MQ=255)
                                                     aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  <  1:4592101/68‑1 (MQ=255)
                                                     aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  <  1:1694742/68‑1 (MQ=255)
                                                     aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGAc                  <  1:1877255/68‑1 (MQ=255)
                                                     aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                          >  1:3547809/1‑44 (MQ=255)
                                                     aCCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                          >  1:657043/1‑44 (MQ=255)
                                                      ccGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGATg                                <  1:2007834/53‑1 (MQ=255)
                                                        gcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa            >  1:2143009/1‑71 (MQ=255)
                                                         cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTa            >  1:3728797/1‑70 (MQ=255)
                                                         cgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc           <  1:2486915/71‑1 (MQ=255)
                                                                tttGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                        <  1:4366415/35‑1 (MQ=255)
                                                                tttGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                        <  1:3443788/35‑1 (MQ=255)
                                                                  tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                   >  1:5434985/1‑38 (MQ=255)
                                                                  tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAg                                   >  1:786608/1‑38 (MQ=255)
                                                                  tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                 >  1:4855383/1‑40 (MQ=255)
                                                                  tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                      >  1:4375949/1‑51 (MQ=255)
                                                                     |                                                                   
CGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG  >  minE/835142‑835278

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