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 836,023 C→T 32.5% C247C (TGC→TGT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,0230CT32.5% 100.8 / 68.0 86C247C (TGC→TGT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (20/38);  new base T (16/12);  total (36/50)
Fisher's exact test for biased strand distribution p-value = 6.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.74e-01

TCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCT  >  minE/835953‑836091
                                                                      |                                                                    
tCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGc                                                                      <  1:4894376/71‑1 (MQ=255)
 cACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGc                                                                      >  1:4567232/1‑70 (MQ=255)
  aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                                    >  1:1327085/1‑71 (MQ=255)
  aCTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                                    >  1:4679511/1‑71 (MQ=255)
    tGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCt                                                                     <  1:1762226/68‑1 (MQ=255)
     ggATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTAt                                                                   >  1:1794705/1‑69 (MQ=255)
     ggATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATcc                                                                 >  1:563713/1‑71 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:1200793/3‑70 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:3361669/3‑70 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:4130164/3‑70 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:1697622/3‑70 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:1433109/3‑70 (MQ=255)
         gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                              >  1:5212552/3‑70 (MQ=255)
          tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                             <  1:4161664/69‑2 (MQ=255)
          tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                             <  1:5500711/69‑2 (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)
                cAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTa                                                                    >  1:3127156/1‑57 (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)
                            cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTac                                                                   >  1:2908237/1‑45 (MQ=255)
                            cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGagtc                                                     >  1:640696/1‑57 (MQ=255)
                            cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAAcc                                            <  1:3325358/69‑1 (MQ=255)
                             ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                                    <  1:2488452/44‑1 (MQ=255)
                             ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                                    <  1:2808234/44‑1 (MQ=255)
                             ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                                    <  1:4537458/44‑1 (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)
                               cAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTacc                                                                  >  1:218124/1‑42 (MQ=16)
                                aaCTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCg                                       <  1:1274678/70‑1 (MQ=255)
                                 aCTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCcg                                                                <  1:5354137/44‑1 (MQ=255)
                                   tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCTGCGTATTGa                                                        <  1:4650891/50‑1 (MQ=255)
                                   tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                        <  1:3360763/50‑1 (MQ=255)
                                   tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                        <  1:1284842/50‑1 (MQ=255)
                                   tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                        <  1:566801/50‑1 (MQ=255)
                                   tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                                        <  1:42145/50‑1 (MQ=255)
                                   tGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAtt                                                          <  1:4161880/48‑1 (MQ=255)
                                    ggAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAACCGACCGTGTGc                                  >  1:1181434/1‑71 (MQ=255)
                                     gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                      >  1:4733433/1‑50 (MQ=255)
                                     gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                      >  1:1831097/1‑50 (MQ=255)
                                     gAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                                      >  1:3881858/1‑50 (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                                  <  1:4415156/57‑1 (MQ=255)
                                                  tCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                  <  1:3871235/57‑1 (MQ=255)
                                                  tCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGc                                  <  1:3714398/57‑1 (MQ=255)
                                                    tGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCgg                                                   >  1:3008409/1‑38 (MQ=255)
                                                    tGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCgg                                                   >  1:4145982/1‑38 (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        <  1:4443711/71‑1 (MQ=255)
                                                              aTCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCg        <  1:1523005/71‑1 (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)
                                                                      |                                                                    
TCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGTATCCGTTATCT  >  minE/835953‑836091

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