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 836,011 G→A 33.0% K243K (AAG→AAA)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,0110GA33.0% 106.0 / 73.7 91K243K (AAG→AAA) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base G (27/34);  new base A (22/8);  total (49/42)
Fisher's exact test for biased strand distribution p-value = 1.34e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

CGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGT  >  minE/835943‑836080
                                                                    |                                                                     
cGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTg                                                                     >  1:5184138/1‑71 (MQ=255)
  tATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGc                                                                    <  1:1566502/70‑1 (MQ=255)
   ttgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAt                                                                  >  1:2078164/2‑71 (MQ=255)
    tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                                                                       >  1:1521174/1‑65 (MQ=255)
    tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                                                                       <  1:1032385/65‑1 (MQ=255)
    tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                                                                       >  1:1602462/1‑65 (MQ=255)
    tgtgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAg                                                                       >  1:4618052/1‑65 (MQ=255)
    tgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAtc                                                                 >  1:2845228/1‑71 (MQ=255)
    tgtgCATAAGCGGTTGTCCGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCAt                                                                  <  1:1071002/70‑1 (MQ=255)
      tgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGTTAAGTCTGAGAAGTGCAtct                                                                <  1:573285/70‑1 (MQ=255)
      tgCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAtct                                                                >  1:1468494/1‑70 (MQ=255)
        cATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAtcttct                                                             <  1:1729687/71‑1 (MQ=255)
          tCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTg                                                            <  1:4083360/70‑1 (MQ=255)
          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                                                   >  1:3361669/3‑70 (MQ=255)
                   gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   >  1:5212552/3‑70 (MQ=255)
                   gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   >  1:4130164/3‑70 (MQ=255)
                   gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   >  1:1200793/3‑70 (MQ=255)
                   gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   >  1:1697622/3‑70 (MQ=255)
                   gtccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   >  1:1433109/3‑70 (MQ=255)
                    tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGc                                                                    >  1:439229/2‑52 (MQ=255)
                    tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGc                                                                    >  1:146300/2‑52 (MQ=255)
                    tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                  <  1:5500711/69‑2 (MQ=255)
                    tccGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacga                                                  <  1:4161664/69‑2 (MQ=255)
                      cGTACAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAtt                                               <  1:2113350/71‑1 (MQ=255)
                        tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAtgtg                                                                     >  1:2158642/1‑47 (MQ=255)
                        tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTg                                                                     >  1:573306/1‑47 (MQ=255)
                        tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTg                                                                     >  1:3215381/1‑47 (MQ=255)
                        tACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGc                                                                    <  1:4130008/48‑1 (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)
                          cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAt                                                                  >  1:5326631/1‑48 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAt                                                                  >  1:3184983/1‑48 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGaa                                            <  1:2470981/70‑1 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAg                                           >  1:975136/1‑71 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGc                                                                    >  1:2391424/1‑46 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGc                                                                    >  1:5032092/1‑46 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGc                                                                    >  1:2516933/1‑46 (MQ=255)
                          cAAAAAAATCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTa                                                         >  1:3127156/1‑57 (MQ=255)
                            aaaaaaTCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCcacg                                                   <  1:5193543/61‑1 (MQ=255)
                             aaaaaTCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTgt                                                           >  1:5508231/1‑51 (MQ=255)
                              aaaaTCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCggg                                       >  1:4372422/1‑71 (MQ=255)
                               aaaTCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGt                                      <  1:1879659/71‑1 (MQ=255)
                               aaaTCTACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCa                                                                   >  1:3619306/1‑42 (MQ=19)
                                    tACTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAAt                                                >  1:892203/1‑56 (MQ=255)
                                     aCTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGc                                                                    >  1:168946/1‑35 (MQ=255)
                                      cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTac                                                        >  1:2908237/1‑45 (MQ=255)
                                      cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGagtc                                          >  1:640696/1‑57 (MQ=255)
                                      cTTCAACTGGAAAAGCGGCAAGTCAGAAAAATGCATCTTCTGTTACCCACGAATTGAGTCCGGTCAAcc                                 <  1:3325358/69‑1 (MQ=255)
                                       ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                         <  1:2808234/44‑1 (MQ=255)
                                       ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                         <  1:2488452/44‑1 (MQ=255)
                                       ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTa                                                         <  1:4537458/44‑1 (MQ=255)
                                       ttCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTAtt                                               <  1:4046841/54‑1 (MQ=255)
                                         cAACTGGAAGAGCGGTAAGTCTGAGAAGTGCAtctt                                                               >  1:2473592/1‑36 (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                                             <  1:566801/50‑1 (MQ=255)
                                             tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                             <  1:42145/50‑1 (MQ=255)
                                             tGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGa                                             <  1:1284842/50‑1 (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                                           >  1:1831097/1‑50 (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                                        >  1:4145982/1‑38 (MQ=255)
                                                              tGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCgg                                        >  1:3008409/1‑38 (MQ=255)
                                                                agaAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTgtcggt     <  1:4389993/71‑1 (MQ=255)
                                                                agaAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTgtcgg      <  1:508103/70‑1 (MQ=255)
                                                                   aGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGGCGGTCGt  <  1:523969/71‑1 (MQ=255)
                                                                    |                                                                     
CGTATGTGCATCACTGGATGCCCGTACAAAAAAATCTACTTCAACTGGAAGAGCGGTAAGTCTGAGAAGTGCATCTTCTGCTATCCGCGTATTGAAGCGGGTCAGCCGACCGTGTGCTCAGAAACCTGTGTCGGTCGT  >  minE/835943‑836080

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