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 836,026 T→C 32.5% Y248Y (TAT→TAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,0260TC32.5% 84.7 / 62.1 77Y248Y (TAT→TAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (17/35);  new base C (13/12);  total (30/47)
Fisher's exact test for biased strand distribution p-value = 1.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

GGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCTT  >  minE/835958‑836092
                                                                    |                                                                  
ggATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTAt                                                                    >  1:1794705/1‑69 (MQ=255)
ggATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATcc                                                                  >  1:563713/1‑71 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:1200793/3‑70 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:5212552/3‑70 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:1433109/3‑70 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:4130164/3‑70 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:3361669/3‑70 (MQ=255)
    gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               >  1:1697622/3‑70 (MQ=255)
     tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                              <  1:5500711/69‑2 (MQ=255)
     tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                              <  1:4161664/69‑2 (MQ=255)
       cGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAtt                                                           <  1:2113350/71‑1 (MQ=255)
         tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCcgcg                                                               <  1:3612143/65‑1 (MQ=255)
         tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTAt                                                            >  1:5108599/1‑68 (MQ=255)
         tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTAt                                                            >  1:1815495/1‑68 (MQ=255)
         tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:2635482/71‑1 (MQ=255)
          aCAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCcgcg                                                               <  1:3179711/64‑1 (MQ=255)
           cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGaa                                                        <  1:2470981/70‑1 (MQ=255)
           cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                       >  1:975136/1‑71 (MQ=255)
             aaaaaaTCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                               <  1:5193543/61‑1 (MQ=255)
               aaaaTCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCggg                                                   >  1:4372422/1‑71 (MQ=255)
                aaaTCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGt                                                  <  1:1879659/71‑1 (MQ=255)
                     tACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAt                                                            >  1:892203/1‑56 (MQ=255)
                       cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGagtc                                                      >  1:640696/1‑57 (MQ=255)
                       cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAAcc                                             <  1:3325358/69‑1 (MQ=255)
                        ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTAtt                                                           <  1:4046841/54‑1 (MQ=255)
                          cAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAg                                               >  1:1748580/1‑64 (MQ=255)
                          cAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAg                                               >  1:688396/1‑64 (MQ=255)
                          cAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGAGGGTCAg                                               >  1:5459720/1‑64 (MQ=255)
                           aaCTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCg                                        <  1:1274678/70‑1 (MQ=255)
                            aCTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCcg                                                                 <  1:5354137/44‑1 (MQ=255)
                              tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCTGCGTATTGa                                                         <  1:4650891/50‑1 (MQ=255)
                              tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:566801/50‑1 (MQ=255)
                              tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:1284842/50‑1 (MQ=255)
                              tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:42145/50‑1 (MQ=255)
                              tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:3360763/50‑1 (MQ=255)
                              tGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAtt                                                           <  1:4161880/48‑1 (MQ=255)
                               ggAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGc                                   >  1:1181434/1‑71 (MQ=255)
                                gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                       >  1:4733433/1‑50 (MQ=255)
                                gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                       >  1:3881858/1‑50 (MQ=255)
                                gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                       >  1:1831097/1‑50 (MQ=255)
                                gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                   <  1:2373275/70‑1 (MQ=255)
                                     gCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGaa                             <  1:3124529/71‑1 (MQ=255)
                                     gCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGaa                             <  1:2603101/71‑1 (MQ=255)
                                        gTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCg                                        <  1:3512480/57‑1 (MQ=255)
                                         tAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                         <  1:4125431/39‑1 (MQ=255)
                                         tAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGTGTCAGCCGACCGTGTGCTCAGAAACCt                         <  1:3052700/71‑1 (MQ=255)
                                           aGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCg                                                     >  1:807190/1‑41 (MQ=255)
                                           aGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCtgt                       >  1:1209816/1‑71 (MQ=255)
                                           aGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCtgc                       >  1:1711302/1‑70 (MQ=255)
                                             tCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                   <  1:3871235/57‑1 (MQ=255)
                                             tCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                   <  1:4415156/57‑1 (MQ=255)
                                             tCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                   <  1:3714398/57‑1 (MQ=255)
                                               tGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCgg                                                    >  1:4145982/1‑38 (MQ=255)
                                               tGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCgg                                                    >  1:3008409/1‑38 (MQ=255)
                                                 agaAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTgtcggt                 <  1:4389993/71‑1 (MQ=255)
                                                 agaAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTgtcgg                  <  1:508103/70‑1 (MQ=255)
                                                   aaatGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCTGCgtgggtc                >  1:777092/4‑70 (MQ=255)
                                                    aatGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGaa                             <  1:4917612/54‑1 (MQ=255)
                                                    aatGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGaa                             <  1:1557606/54‑1 (MQ=255)
                                                    aatGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCTGCgtgggtcgc              <  1:1656730/69‑2 (MQ=255)
                                                    aGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGGCGGTCGt              <  1:523969/71‑1 (MQ=255)
                                                     atGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCTGCgtgggtcgca             >  1:3327909/2‑69 (MQ=255)
                                                      tGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTAt            <  1:401398/71‑1 (MQ=255)
                                                       gCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAAcc                          <  1:1254123/56‑1 (MQ=255)
                                                         aTCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATcct         <  1:5139350/71‑2 (MQ=255)
                                                         aTCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCg         <  1:1523005/71‑1 (MQ=255)
                                                         aTCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCg         <  1:4443711/71‑1 (MQ=255)
                                                         aTCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAAACTGTGTCGGTCGTATCCg         <  1:566046/71‑1 (MQ=255)
                                                          tcttctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGtgtg                                    <  1:2499695/43‑1 (MQ=255)
                                                           cttctGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGa                              <  1:4473373/48‑1 (MQ=255)
                                                            ttctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTa      >  1:5082527/1‑71 (MQ=255)
                                                             tctGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCTGCGTGGGTCGCATCCGGTAt     >  1:3191624/1‑71 (MQ=255)
                                                             tctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTAt     >  1:58117/1‑71 (MQ=255)
                                                              ctGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGCTCAGAAACCTGCgtgggtcgca             <  1:2475869/62‑3 (MQ=255)
                                                              ctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGtt       <  1:5263314/68‑1 (MQ=255)
                                                              ctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGtt       <  1:675981/68‑1 (MQ=255)
                                                              ctGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTa      <  1:5161340/69‑1 (MQ=255)
                                                                 cTATCCGCGTATTTAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCt   <  1:4448824/69‑1 (MQ=255)
                                                                    tCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCtt  <  1:2269130/67‑1 (MQ=255)
                                                                    tCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCtt  <  1:2319512/67‑1 (MQ=255)
                                                                    |                                                                  
GGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCTT  >  minE/835958‑836092

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