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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 835,031 C→T 16.0% Y1163Y (TAC→TAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,0310CT16.0% 201.7 / 25.9 81Y1163Y (TAC→TAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (33/35);  new base T (7/6);  total (40/41)
Fisher's exact test for biased strand distribution p-value = 7.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

ACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACT  >  minE/834961‑835101
                                                                      |                                                                      
aCAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc                                                                        <  1:2522119/71‑1 (MQ=255)
 cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAcc                                                                       <  1:465427/71‑1 (MQ=255)
 cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc                                                                        >  1:1048619/1‑70 (MQ=255)
 cAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTAc                                                                        >  1:3352417/1‑70 (MQ=255)
    cAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAc                                                                     <  1:1064500/70‑1 (MQ=255)
     aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc                                                                   >  1:2375329/1‑71 (MQ=255)
     aaCGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgc                                                                   <  1:2197837/71‑1 (MQ=255)
      aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  <  1:2606534/71‑1 (MQ=255)
      aCGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  <  1:2548474/71‑1 (MQ=255)
       cGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  <  1:999822/70‑1 (MQ=255)
       cGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCAcgcc                                                                  >  1:2651998/1‑69 (MQ=255)
          tGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                                              <  1:1451599/71‑1 (MQ=255)
           gCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAgg                                                              >  1:2691125/1‑70 (MQ=255)
            ctctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCTCAGGa                                                             <  1:2769790/70‑1 (MQ=255)
            ctctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGa                                                             <  1:3419235/70‑1 (MQ=255)
              ctGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                                          >  1:2245694/1‑71 (MQ=255)
               tGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACg                                                          >  1:2452496/1‑70 (MQ=255)
                 aCTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                                        <  1:3343759/70‑1 (MQ=255)
                 aCTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTAt                                                       <  1:2340125/71‑1 (MQ=255)
                 aCTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTAt                                                       <  1:3157499/71‑1 (MQ=255)
                 aCTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                                       >  1:2705619/1‑71 (MQ=255)
                  cTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATc                                                      <  1:3439265/71‑1 (MQ=255)
                  cTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAtt                                                      <  1:1094271/71‑2 (MQ=255)
                  cTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAtt                                                      <  1:2391046/71‑2 (MQ=255)
                  cTGCCCGCGCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACGCAt                                                       >  1:1391483/1‑70 (MQ=255)
                   tGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                                                     >  1:3326240/1‑71 (MQ=255)
                   tGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                                                     >  1:1554806/1‑71 (MQ=255)
                     cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:3189789/71‑1 (MQ=255)
                     cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:3282058/71‑1 (MQ=255)
                     cccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGtt                                                   <  1:3185670/71‑1 (MQ=255)
                      ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:1291355/71‑1 (MQ=255)
                      ccGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:2400344/71‑1 (MQ=255)
                        gTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAc                                                >  1:243385/1‑71 (MQ=255)
                         tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  <  1:1470713/52‑1 (MQ=255)
                         tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                                               >  1:218630/1‑71 (MQ=255)
                         tGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcc                                               >  1:3059265/1‑71 (MQ=255)
                         cgCGGTGGTCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGaa                                                            >  1:3400297/2‑58 (MQ=255)
                           cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                                             <  1:104930/71‑1 (MQ=255)
                           cGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctg                                             >  1:3925061/1‑71 (MQ=255)
                              ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCAcgcg                                                                  <  1:1695276/47‑1 (MQ=255)
                              ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                                         <  1:1402295/56‑1 (MQ=255)
                              ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGt                                                         <  1:2749344/56‑1 (MQ=255)
                              ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTa                                                        >  1:1742048/1‑57 (MQ=255)
                              ttGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAAcctgcc                                           <  1:456491/70‑1 (MQ=255)
                                gTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCa                                                                >  1:2524787/1‑47 (MQ=255)
                                 tCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGt                                       <  1:2091218/71‑1 (MQ=255)
                                 tCAGCCAACGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACgca                                                        <  1:3557089/54‑3 (MQ=16)
                                   agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:3278299/1‑71 (MQ=255)
                                   agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:3273817/1‑71 (MQ=255)
                                   agccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTc                                     >  1:1489476/1‑71 (MQ=255)
                                   agccaacGTGTACCGCCGGGCATGACCATGATGTATCAcgccc                                                                 >  1:50181/1‑41 (MQ=12)
                                    ggcagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTa                                                  <  1:1995826/55‑1 (MQ=255)
                                    gccaacGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAACgca                                                        <  1:1784727/51‑3 (MQ=16)
                                     ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   <  1:835364/71‑1 (MQ=255)
                                     ccagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCg                                    >  1:525714/1‑70 (MQ=255)
                                      cagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  <  1:3941251/71‑1 (MQ=255)
                                      cagcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  <  1:3403729/71‑1 (MQ=255)
                                       agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAAc                                                           >  1:2446594/1‑45 (MQ=255)
                                       agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCGTGGTTCGGa                                  >  1:3309073/1‑70 (MQ=255)
                                       agcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGa                                  >  1:2686197/1‑70 (MQ=255)
                                        gcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGaaa                                >  1:1025423/1‑71 (MQ=255)
                                        gcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGaaa                                >  1:452458/1‑71 (MQ=255)
                                        gcGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGaa                                 >  1:2592330/1‑70 (MQ=255)
                                        acGTGTACCGCCGGGCATGACCATGATGTATCACGCCCAGGAAc                                                           >  1:341739/2‑44 (MQ=12)
                                           tgtTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCg                                                     <  1:1959701/47‑1 (MQ=255)
                                             ttCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc                           <  1:3672553/71‑1 (MQ=255)
                                              tCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc                           >  1:1647102/1‑70 (MQ=255)
                                                  gCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCaa                        >  1:1402724/1‑69 (MQ=255)
                                                   cAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTAcc                           >  1:221613/1‑65 (MQ=255)
                                                     gggATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCg                   <  1:844662/71‑1 (MQ=255)
                                                       gATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                                        >  1:2200799/1‑48 (MQ=255)
                                                       gATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                                        >  1:2874356/1‑48 (MQ=255)
                                                       gATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                                        >  1:2793152/1‑48 (MQ=255)
                                                       gATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTgg                                        >  1:2290329/1‑48 (MQ=255)
                                                        aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:1101220/71‑1 (MQ=255)
                                                        aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:3771756/71‑1 (MQ=255)
                                                        aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:2164449/71‑1 (MQ=255)
                                                        aTGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCgtgg                <  1:3122065/71‑1 (MQ=255)
                                                             cATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAAtt                              <  1:1157023/52‑1 (MQ=255)
                                                             cATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTa           <  1:1234739/71‑1 (MQ=255)
                                                               tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATc         >  1:3120981/1‑71 (MQ=255)
                                                               tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATc         >  1:2986390/1‑71 (MQ=255)
                                                               tgatgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATc         >  1:1000756/1‑71 (MQ=255)
                                                                 atgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   >  1:3721370/1‑43 (MQ=255)
                                                                 atgTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCgg                                   >  1:2121662/1‑43 (MQ=255)
                                                                      ccACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCg                                    >  1:3728666/1‑37 (MQ=255)
                                                                      ccACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACt  >  1:3900272/1‑71 (MQ=255)
                                                                      |                                                                      
ACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGATGACCATGATGTACCACGCGCAGGAACGTATCGTTAACCTGCCTGGTTCGGAAATTACCCAACAGCGTGGTGGTATCCATAACT  >  minE/834961‑835101

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