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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,912,429 C→T 47.8% A135T (GCG→ACG)  pyrI ← aspartate carbamoyltransferase, regulatory subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,912,4290CT47.8% 20.7 / 165.0 113A135T (GCG→ACG) pyrIaspartate carbamoyltransferase, regulatory subunit
Reads supporting (aligned to +/- strand):  ref base C (37/22);  new base T (31/23);  total (68/45)
Fisher's exact test for biased strand distribution p-value = 7.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 114 total aligned reads displayed.

CCGCAATTAATTGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAGTTG  >  minE/2912364‑2912496
                                                                 |                                                                   
  gCAATTAATTGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCa                                                              >  1:436346/1‑71 (MQ=255)
  gCAATTAATTGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCa                                                              >  1:118673/1‑71 (MQ=255)
  gCAATTAATTGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCa                                                              >  1:2370881/1‑71 (MQ=255)
    aattaattGGCTAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCAtt                                                            <  1:369509/71‑1 (MQ=255)
        aattGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgcg                                                        >  1:840397/1‑71 (MQ=255)
        aattGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgc                                                         <  1:3969217/70‑1 (MQ=255)
         attGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgcgc                                                       <  1:1585415/71‑1 (MQ=255)
         attGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgcgc                                                       <  1:2135318/71‑1 (MQ=255)
         attGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgc                                                         <  1:3084999/69‑1 (MQ=255)
         attGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGgc                                                         <  1:682148/69‑1 (MQ=255)
            ggCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGt                                                     <  1:1172031/70‑1 (MQ=255)
             gCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   <  1:3569455/71‑1 (MQ=255)
             gCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   <  1:861940/71‑1 (MQ=255)
             gCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   <  1:2056069/71‑1 (MQ=255)
              ccAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   <  1:1075157/70‑1 (MQ=255)
                aGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTCCg                                                <  1:1822571/71‑1 (MQ=255)
                 gCACCATATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGCGCGTGATATCATTGGCGCGttt                                                   <  1:1878250/67‑1 (MQ=255)
                  caccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCa                                              <  1:4047246/71‑1 (MQ=255)
                   accacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCa                                                              <  1:3997554/54‑1 (MQ=255)
                   accacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCAc                                             >  1:3302360/1‑71 (MQ=255)
                    ccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATc                                                               <  1:3633670/52‑1 (MQ=255)
                    ccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATc                                                               <  1:2828341/52‑1 (MQ=255)
                    ccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGgcgc                                                       <  1:2077998/60‑1 (MQ=255)
                    ccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGgcgc                                                       <  1:1757660/60‑1 (MQ=255)
                    ccacATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGcgcg                                                      <  1:2896592/61‑1 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAt                                                             >  1:2908922/1‑52 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAt                                                             >  1:2046907/1‑52 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAt                                                             >  1:2804427/1‑52 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAt                                                             >  1:3334528/1‑52 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAt                                                             >  1:455945/1‑52 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACgg                                           >  1:3960362/1‑70 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACgg                                           >  1:668605/1‑70 (MQ=255)
                      acaTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACgg                                           >  1:1143561/1‑70 (MQ=255)
                       caTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGa                                                                   >  1:1784813/1‑45 (MQ=255)
                        aTTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGAGTGatat                                                                <  1:1455024/47‑1 (MQ=255)
                         ttATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGcgcg                                                      <  1:219761/56‑1 (MQ=255)
                          tATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:2450590/1‑71 (MQ=255)
                           aTGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCAtt                                                            >  1:2673116/1‑48 (MQ=255)
                           aTGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGc                                     >  1:4021626/1‑71 (MQ=255)
                              ggAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGa                                                                   >  1:1529697/1‑38 (MQ=255)
                              ggAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGa                                                                   >  1:2538891/1‑38 (MQ=255)
                              ggAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGa                                                                   >  1:2582034/1‑38 (MQ=255)
                              ggAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   >  1:2553916/1‑70 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCa                                                              >  1:900030/1‑40 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGAt                                >  1:1652956/1‑70 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGtt                                                    >  1:2671179/1‑50 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGtt                                                    >  1:4187364/1‑50 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGtt                                                    >  1:803448/1‑50 (MQ=255)
                                 aaaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGtt                                                    >  1:3890782/1‑50 (MQ=255)
                                  aaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGa                              <  1:4227492/71‑1 (MQ=255)
                                  aaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGa                              <  1:3138526/71‑1 (MQ=255)
                                  aaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGa                              <  1:1708498/71‑1 (MQ=255)
                                  aaCTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGa                              <  1:3047552/71‑1 (MQ=255)
                                    ctctTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:2395299/1‑61 (MQ=255)
                                    ctctTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:1326636/1‑61 (MQ=255)
                                    ctctTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:3134875/1‑61 (MQ=255)
                                    ctctTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:1934348/1‑61 (MQ=255)
                                    ctctTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAg                                      >  1:4060631/1‑61 (MQ=255)
                                       tttttCACAGTTTTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   >  1:3777811/1‑61 (MQ=255)
                                       tttttCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   >  1:1912493/1‑61 (MQ=255)
                                       tttttCACAGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   >  1:3430056/1‑61 (MQ=255)
                                       tttttCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCATTTTCGCACGGCAAAGCTGGATGAAACCg                         >  1:2019096/1‑71 (MQ=255)
                                            cacaGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCaa                                        <  1:2313144/51‑1 (MQ=255)
                                             acaGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGTAAAGCTGGATGAAACCGGTTCg                    <  1:1420690/70‑1 (MQ=255)
                                             acaGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   <  1:3147821/55‑1 (MQ=255)
                                             acaGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   <  1:2519950/55‑1 (MQ=255)
                                             acaGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   <  1:1391685/55‑1 (MQ=255)
                                             acaGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCgg                   <  1:1307790/71‑1 (MQ=255)
                                              caGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCgg                   >  1:1901573/1‑70 (MQ=255)
                                               aGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   <  1:2475649/53‑1 (MQ=255)
                                               aGTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGa                                 >  1:324115/1‑55 (MQ=255)
                                               aGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCa                 <  1:2909288/71‑1 (MQ=255)
                                                gTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTg                                   <  1:951669/52‑1 (MQ=255)
                                                gTATTTGCATTTGAGCGTGATATCATTGGCGCGTTTTCCCACGGCAAAGCTg                                   <  1:1359983/52‑1 (MQ=255)
                                                 tATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   >  1:1060371/1‑35 (MQ=255)
                                                 tATTTGCATTTGAGCGCGATATCATTGGCGCGttt                                                   >  1:1194761/1‑35 (MQ=255)
                                                  aTTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATgg              >  1:1056139/1‑71 (MQ=255)
                                                   tttGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGc             >  1:3848329/1‑71 (MQ=255)
                                                   tttGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGc             >  1:3277686/1‑71 (MQ=255)
                                                   tttGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGc             >  1:253654/1‑71 (MQ=255)
                                                   tttGCATTTGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGc             >  1:2809653/1‑71 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACg                                            >  1:3507074/1‑40 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGaaa                            >  1:4166431/1‑56 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGaaa                            >  1:485950/1‑56 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGaaa                            >  1:2709495/1‑56 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGaaa                            >  1:31893/1‑56 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGc                  >  1:3319483/1‑66 (MQ=255)
                                                   tttGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCa                 >  1:2921050/1‑67 (MQ=255)
                                                       cATTTGAGCGCTATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGa          >  1:2286444/1‑70 (MQ=255)
                                                       cATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGa          >  1:1125212/1‑70 (MQ=255)
                                                         tttGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATAc       <  1:2796233/71‑1 (MQ=255)
                                                         tttGAGCGCGATATCATTTGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGa          <  1:3526899/68‑1 (MQ=255)
                                                         tttGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATTGCTGa          <  1:414035/68‑1 (MQ=255)
                                                         tttGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGa          <  1:3612187/68‑1 (MQ=255)
                                                          ttGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGa          <  1:603826/67‑1 (MQ=255)
                                                           tGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAg     >  1:2716006/1‑71 (MQ=255)
                                                           tGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAg     >  1:283400/1‑71 (MQ=255)
                                                           tGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAg     >  1:2183825/1‑71 (MQ=255)
                                                           tGAGCGTGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAg     >  1:3868776/1‑71 (MQ=255)
                                                              gcgtGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAGTTg  <  1:3105036/71‑1 (MQ=255)
                                                                 |                                                                   
CCGCAATTAATTGGCCAGCACCACATTATGGGAAAACTCTTTTTCACAGTATTTGCATTTGAGCGCGATATCATTGGCGCGTTTTCGCACGGCAAAGCTGGATGAAACCGGTTCGGCATGGCTGATACAGTTG  >  minE/2912364‑2912496

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A