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
A3 F2 I1 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 Exported 834,040 A→C 25.4% K833T (AAA→ACA) ‡ narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported834,0400AC25.4% 71.9 / 40.8 59K833T (AAA→ACA) ‡narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (28/16);  new base C (5/10);  total (33/26)
Fisher's exact test for biased strand distribution p-value = 6.93e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCGATCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAGCATGA  >  Exported/833982‑834109
                                                          |                                                                     
gTCGATCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAgt                                                           <  1:593408/71‑1 (MQ=255)
  cGATCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGaaa                                                                      >  1:3149122/1‑58 (MQ=255)
   gATCCGGCGTGGGAATCACGCAGCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGtgtg                                                        <  1:4110679/71‑1 (MQ=255)
    aTCCGGCGTGGGAATCACGCAGCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGc                                                       <  1:1316784/71‑1 (MQ=255)
    aTCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAgtgt                                                         <  1:2696619/69‑1 (MQ=255)
    aTCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGc                                                       >  1:217339/1‑71 (MQ=255)
     tCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCg                                                      >  1:1222129/1‑71 (MQ=255)
     tCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCg                                                      >  1:1893072/1‑71 (MQ=255)
      ccGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGt                                                     >  1:3690035/1‑71 (MQ=255)
       cGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGt                                                     <  1:5064572/70‑1 (MQ=255)
                   cGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTggg                                         >  1:4726129/1‑70 (MQ=255)
                    gAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGa                                                              <  1:5235413/48‑1 (MQ=255)
                    gAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGt                                        >  1:2200177/1‑70 (MQ=255)
                      gcaGCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGCGTCATCTTGGCaaa                                     <  1:540376/69‑1 (MQ=255)
                      aaaGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATtctc                                                                 >  1:3297926/1‑43 (MQ=255)
                      aaaGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTa                                       >  1:1998257/1‑69 (MQ=255)
                       aaGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTa                                       >  1:3336904/1‑68 (MQ=255)
                       aaGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAg                                    <  1:3145946/71‑1 (MQ=255)
                       aaGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAg                                    <  1:2508654/71‑1 (MQ=255)
                        aGCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGTCAAAGa                                   <  1:729744/71‑1 (MQ=255)
                         gCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGtgtg                                                        <  1:5248954/49‑1 (MQ=255)
                         gCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCaaa                                     <  1:1676309/68‑1 (MQ=255)
                         gCGACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCaaa                                     <  1:2248638/68‑1 (MQ=255)
                           gACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGa                                   >  1:3940128/1‑68 (MQ=255)
                           gACTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGa                                   >  1:3160282/1‑68 (MQ=255)
                            aCTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAAcc                               <  1:3537040/71‑1 (MQ=255)
                             cTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCg                                                      >  1:4321152/1‑47 (MQ=255)
                             cTGGGAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGCTCATCTTGGCAAAGAAAc                                >  1:2743144/1‑69 (MQ=255)
                               gggAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGAAACCGAc                            >  1:4552370/1‑71 (MQ=255)
                                ggAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGAAACCGAc                            <  1:2258563/70‑1 (MQ=255)
                                ggAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGAAACCGAc                            <  1:2783832/70‑1 (MQ=255)
                                ggAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAgtgt                                                         >  1:5436248/1‑41 (MQ=255)
                                ggAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGAc                            <  1:2862128/70‑1 (MQ=255)
                                 gAAATCTACAAAGGTATCGCCAAAGCATTTTCGCAAGTGTGCGTGGGTCATCTTGGCAAAGAAACCGAcgt                          <  1:2618031/71‑3 (MQ=255)
                                    aTCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGAc                            <  1:4122724/66‑1 (MQ=255)
                                     tCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGt                       <  1:2503888/70‑1 (MQ=255)
                                      cTACAAAGCCATCGCGAAGAAATTCTCCGAAgtgt                                                         >  1:2171580/1‑35 (MQ=255)
                                      cTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGa                                   >  1:4100183/1‑57 (MQ=255)
                                      cTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACAt                          >  1:1844271/1‑66 (MQ=255)
                                      cTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCa                     >  1:5401601/1‑71 (MQ=255)
                                       tACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGa                             >  1:1545818/1‑62 (MQ=255)
                                       tACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCAc                    >  1:2226527/1‑71 (MQ=255)
                                        aCAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGt                                                     >  1:2651771/1‑37 (MQ=255)
                                        aCAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCa                     >  1:2529147/1‑69 (MQ=255)
                                         cAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCAc                    <  1:1865711/69‑1 (MQ=255)
                                         cAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACg                   >  1:1021126/1‑70 (MQ=255)
                                         cAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGc                  <  1:2239059/71‑1 (MQ=255)
                                          aaaGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCg                              <  1:252611/58‑1 (MQ=255)
                                          aaaGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCg                              <  1:4628610/58‑1 (MQ=255)
                                          aaaGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCg                              <  1:1063994/58‑1 (MQ=255)
                                           aaGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     >  1:1495186/1‑50 (MQ=255)
                                           aaGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     >  1:645874/1‑50 (MQ=255)
                                                 tCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATc                         <  1:4375163/56‑1 (MQ=255)
                                                  cgcgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATc          >  1:4370572/1‑70 (MQ=255)
                                                   gcgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACAt                          >  1:3755340/1‑53 (MQ=255)
                                                   gcgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACAt                          >  1:1707007/1‑53 (MQ=255)
                                                   gcgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATc          >  1:2810237/1‑69 (MQ=255)
                                                   gcgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATc          >  1:226926/1‑69 (MQ=255)
                                                    cgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     >  1:5557138/1‑41 (MQ=255)
                                                    cgAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAg       >  1:1941701/1‑71 (MQ=255)
                                                       agaaATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCa                     >  1:4731918/1‑54 (MQ=255)
                                                       agaaATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAGCAt    <  1:2440358/71‑1 (MQ=255)
                                                        gaaATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAGCAt    <  1:1024992/70‑1 (MQ=255)
                                                         aaaTTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     <  1:4792115/36‑1 (MQ=255)
                                                         aaaTTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     <  1:3509166/36‑1 (MQ=255)
                                                         aaaTTCTCCGAAGTGTGCGTCGGCCATCTGGGTaaa                                     <  1:1826759/36‑1 (MQ=255)
                                                         aaaTTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAGCATGa  <  1:4965660/71‑1 (MQ=255)
                                                          |                                                                     
GTCGATCCGGCCTGGGAAGCGAAAAGCGACTGGGAAATCTACAAAGCCATCGCGAAGAAATTCTCCGAAGTGTGCGTCGGCCATCTGGGTAAAGAAACCGACATCGTCACGCTGCCTATCCAGCATGA  >  Exported/833982‑834109

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