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 982,620 C→A 25.0% G22G (GGC→GGA)  ydfA → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE982,6200CA25.0% 342.1 / 84.3 160G22G (GGC→GGA) ydfAhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (56/64);  new base A (15/25);  total (71/89)
Fisher's exact test for biased strand distribution p-value = 3.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.15e-01

Only 100 of 166 total aligned reads displayed.

AGCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGG  >  minE/982552‑982686
                                                                    |                                                                  
aGCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCAc                                                                  >  1:4293902/1‑71 (MQ=255)
aGCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCAc                                                                  >  1:4859633/1‑71 (MQ=255)
 gCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACg                                                                 <  1:5078245/71‑1 (MQ=255)
 gCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTAAGGCGTGTTTCCAAACCAGGACGGCACg                                                                 <  1:3760797/71‑1 (MQ=255)
   aTGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGtt                                                               <  1:1904906/71‑1 (MQ=255)
    tGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTc                                                              <  1:3036222/71‑1 (MQ=255)
    tGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTc                                                              <  1:347761/71‑1 (MQ=255)
      gATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCAc                                                            <  1:2359212/71‑1 (MQ=255)
      gATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCAc                                                            <  1:2339448/71‑1 (MQ=255)
       aTACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCAcc                                                           >  1:93754/1‑71 (MQ=255)
        tACTATCGATCTTGGCAACAACGAATCTCTGGTGTACTGCGTGTTTCCAAACCAGGACGGCACGTTCACCg                                                          <  1:1293860/71‑1 (MQ=255)
          cTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTc                                                              >  1:51302/1‑65 (MQ=255)
          cTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGc                                                         <  1:3261743/70‑1 (MQ=255)
          cTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGc                                                         <  1:5578374/70‑1 (MQ=255)
          cTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGc                                                         <  1:4439219/70‑1 (MQ=255)
           aaTCGACCTCGGCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGTAACGTTCACTGcc                                                        >  1:2488450/2‑69 (MQ=255)
           aaTCGACCTCGGCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGcca                                                       >  1:5656746/2‑69 (MQ=255)
            aTCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAAt                                                      >  1:4801204/1‑71 (MQ=255)
             tCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGtt                                                               >  1:103855/1‑61 (MQ=255)
              cGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATg                                                     >  1:2933886/1‑70 (MQ=255)
              cGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGa                                                    >  1:3132958/1‑71 (MQ=255)
               gATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGAc                                                   >  1:1627117/1‑71 (MQ=255)
                  ctcggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACg                                                  <  1:2015484/66‑1 (MQ=255)
                  ctcggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACg                                                  <  1:3665795/66‑1 (MQ=255)
                  cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                >  1:4769378/1‑71 (MQ=255)
                  cTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                >  1:1714743/1‑71 (MQ=255)
                    tGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGtata                                              >  1:4917035/1‑71 (MQ=255)
                    cggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGa                                                    >  1:1535482/2‑65 (MQ=255)
                    cggCAACAACGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGa                                                    >  1:2261816/2‑65 (MQ=255)
                     ggCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCAGGTTCACCGCAATGACGTATAc                                             >  1:5165757/1‑71 (MQ=255)
                     ggCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCa                                                             >  1:5368935/1‑55 (MQ=255)
                     ggCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                  <  1:1106693/66‑1 (MQ=255)
                       caacaaCGAATCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTc                                                              >  1:1368259/1‑52 (MQ=255)
                        aacaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaa                                          <  1:5425847/71‑1 (MQ=255)
                         acaacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCaaa                                         <  1:3543836/71‑1 (MQ=255)
                           aacGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCaa                                                       >  1:1635342/1‑55 (MQ=255)
                              gAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaa                                    <  1:411584/71‑1 (MQ=255)
                              gAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaa                                    <  1:348569/71‑1 (MQ=255)
                                aTCCCTGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaaaa                                  <  1:5534185/71‑1 (MQ=255)
                                 tctcTGGTGTACGGCGTGTTTCCAAACCAGGACGGc                                                                    <  1:672586/36‑1 (MQ=255)
                                 tctcTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGc                                      <  1:4885688/66‑1 (MQ=255)
                                 tccctGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaa                                    <  1:3567720/65‑1 (MQ=255)
                                 tccctGGTGTGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCaa                                    <  1:1763209/65‑1 (MQ=255)
                                  ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                   >  1:1740954/1‑68 (MQ=255)
                                  ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                   >  1:2656630/1‑68 (MQ=255)
                                  ctctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaa                                   >  1:2412398/1‑68 (MQ=255)
                                   tctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGtt                                                               >  1:4400558/1‑39 (MQ=255)
                                   tctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGtata                                              >  1:1169894/1‑56 (MQ=255)
                                     tGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                <  1:1984123/68‑1 (MQ=255)
                                       gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                             <  1:2964101/69‑1 (MQ=255)
                                       gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTa                            <  1:312039/70‑1 (MQ=255)
                                       gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                           <  1:3155242/71‑1 (MQ=255)
                                       gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                           <  1:5059234/71‑1 (MQ=255)
                                       gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTa                            >  1:5248812/1‑70 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                          <  1:4275073/71‑1 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                          <  1:4568437/71‑1 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                          <  1:718535/71‑1 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                          <  1:3289837/71‑1 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                           >  1:1653029/1‑70 (MQ=255)
                                        tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                           >  1:2696590/1‑70 (MQ=255)
                                        tgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaaa                          <  1:5295608/71‑1 (MQ=255)
                                            cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCaa                                                       >  1:3903751/1‑38 (MQ=255)
                                            cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCaa                                                       >  1:1703812/1‑38 (MQ=255)
                                            cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                      <  1:4455141/71‑1 (MQ=255)
                                            cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                      <  1:2442740/71‑1 (MQ=255)
                                            cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAAcc                       >  1:591429/1‑70 (MQ=255)
                                            cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCg                      <  1:1420245/71‑1 (MQ=255)
                                             ggCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                  <  1:3771331/42‑1 (MQ=255)
                                             ggCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACg                                                  <  1:2668792/42‑1 (MQ=255)
                                             ggCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGa                     <  1:3707637/71‑1 (MQ=255)
                                             ggCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGa                     <  1:2237662/71‑1 (MQ=255)
                                             ggCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGa                     <  1:4184449/71‑1 (MQ=255)
                                               cGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaaa                   <  1:1957919/71‑1 (MQ=255)
                                               cGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                   >  1:2098552/1‑71 (MQ=255)
                                                 tgtTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaaa                         >  1:2095174/1‑63 (MQ=255)
                                                   tttCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGttt                             >  1:4496144/1‑57 (MQ=255)
                                                     tCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                >  1:5614570/1‑36 (MQ=255)
                                                     tCCAAACCAGGACGGCACGTTCACCGCAATGACGta                                                >  1:1068631/1‑36 (MQ=255)
                                                     tCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaaaa                         >  1:3939251/1‑59 (MQ=255)
                                                       cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc           >  1:5012760/1‑71 (MQ=255)
                                                       cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc           >  1:4718072/1‑71 (MQ=255)
                                                       cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc           >  1:578358/1‑71 (MQ=255)
                                                       cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGc            <  1:1448562/70‑1 (MQ=255)
                                                        caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                             >  1:2897144/2‑52 (MQ=255)
                                                        caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                             >  1:3571703/2‑52 (MQ=255)
                                                        caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                             >  1:5544429/2‑52 (MQ=255)
                                                        caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                             >  1:1347487/2‑52 (MQ=255)
                                                         aaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGcgcg         <  1:5188924/71‑1 (MQ=255)
                                                         aaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGcgcg         <  1:4637559/71‑1 (MQ=255)
                                                         aaCCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCg         >  1:4722547/1‑71 (MQ=255)
                                                             aGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCga     <  1:3247907/71‑2 (MQ=255)
                                                             aGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                    <  1:2312492/56‑1 (MQ=255)
                                                             aGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                    <  1:4531709/56‑1 (MQ=255)
                                                               gACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaaa                                  >  1:2560055/1‑40 (MQ=255)
                                                               gACGGCACGTTCACCGCAATGACGTATACCAAAAGCaaaa                                  >  1:4873118/1‑40 (MQ=255)
                                                               gACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                    <  1:667521/54‑1 (MQ=255)
                                                                aCGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCgctgg  <  1:3627447/71‑1 (MQ=255)
                                                                    cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                    <  1:131105/49‑1 (MQ=255)
                                                                    cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                    <  1:1800783/49‑1 (MQ=255)
                                                                    cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAAt                 <  1:724862/52‑1 (MQ=255)
                                                                    |                                                                  
AGCATGGATACTATCGATCTTGGCAACAACGAATCTCTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGG  >  minE/982552‑982686

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