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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,664,111 A→G 26.8% E365E (GAA→GAG)  rtcB → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,664,1110AG26.8% 144.0 / 54.3 130E365E (GAA→GAG) rtcBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (26/69);  new base G (9/26);  total (35/95)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.68e-01

Only 100 of 130 total aligned reads displayed.

AGCCGAACTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGA  >  minE/2664046‑2664175
                                                                 |                                                                
 gCCGAACTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGc                                                               <  1:2269985/68‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:849353/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:2167755/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:2168311/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:1470777/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:3435184/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:1092908/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:1718572/69‑1 (MQ=255)
      aCTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCAACGCGCATGTGGAATGCCGTaaa                                                         <  1:604991/69‑1 (MQ=255)
        tAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:1055688/67‑1 (MQ=255)
         aaaGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGa                                                       >  1:2368970/1‑68 (MQ=255)
         aaaGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGAt                                                      >  1:2359818/1‑69 (MQ=255)
           aGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGACACCGCGCATGTGGAATGCCGTAAAGa                                                       >  1:3044764/1‑66 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCTCCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:3324780/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:57112/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:1862759/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:2092924/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:62608/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:611429/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:248441/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:2526938/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:2596575/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:269418/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:2752991/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:2772285/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:915278/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:744524/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:83337/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:1441018/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:1252901/69‑1 (MQ=255)
                  aaaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:1518255/69‑1 (MQ=255)
                  aaaCTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTg                                             <  1:1742167/69‑1 (MQ=255)
                  aaaCTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTg                                             <  1:1094873/69‑1 (MQ=255)
                  aaaCTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTg                                             <  1:3223149/69‑1 (MQ=255)
                  aaaCTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTg                                             <  1:2137873/69‑1 (MQ=255)
                   aaCTGTTCAGTGTGGAAGATCAAATCCGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTg                                             <  1:3088167/68‑1 (MQ=255)
                          cAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:892558/69‑1 (MQ=255)
                          cAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:3183916/1‑69 (MQ=255)
                          cAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:1105733/1‑69 (MQ=255)
                          cAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:287603/1‑69 (MQ=255)
                          cAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:818359/1‑69 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:3164908/1‑60 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:1340188/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:3176446/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:118923/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:2683461/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:1817821/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     >  1:1502619/1‑60 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:1581405/60‑1 (MQ=255)
                                   aGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATcgacga                                     <  1:1780043/60‑1 (MQ=255)
                                     aTCAAATTCGTGCCACCGCGCATGTGGAATGCCGTaaa                                                         <  1:487621/38‑1 (MQ=255)
                                       cAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCg                        >  1:1469682/1‑69 (MQ=255)
                                             cGTGCCACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATaaa                  <  1:1907338/69‑1 (MQ=255)
                                             cGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      >  1:1993731/1‑65 (MQ=255)
                                             cGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      >  1:2472249/1‑65 (MQ=255)
                                             cGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      >  1:614224/1‑65 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:434505/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:2006088/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:1516802/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:776836/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:2701969/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGata              >  1:1073364/1‑68 (MQ=255)
                                                  cACCGCGCATGTGGAGTGCCGTAAAGATGCCGAGGTGATCGACGAAATCCCGATGGCGTATAAAGat               >  1:1046120/1‑67 (MQ=255)
                                                   aCCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATAtt            <  1:2122163/69‑1 (MQ=255)
                                                           tgtgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:1634910/69‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:1008592/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:51863/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:706687/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:2501553/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:3131348/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:1307459/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:1212417/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:1201055/40‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:3158040/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:2485190/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:2458406/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:1290134/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:186636/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:2408913/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:3377167/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:2230773/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:196277/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:1924665/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGta                      <  1:1921600/49‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    >  1:990225/1‑67 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:3231815/67‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    >  1:3224424/1‑67 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:3130450/67‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:2562760/67‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:295797/67‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:2717046/67‑1 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGa  >  1:1920533/1‑69 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGa  >  1:630786/1‑69 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGa  >  1:2508357/1‑69 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGa  >  1:874947/1‑69 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGa  >  1:2766817/1‑69 (MQ=255)
                                                             tgGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATACCGATGGCGTATAAAGATATTGATGCGGt    >  1:962891/1‑67 (MQ=255)
                                                             tgGAATGCCGTAAAGATGACGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    >  1:2437604/1‑67 (MQ=255)
                                                              ggAATGCCGTAAAGATGCCGAAGTGATCGACGAAATccc                               <  1:1665573/39‑1 (MQ=255)
                                                              ggAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGt    <  1:1875524/66‑1 (MQ=255)
                                                                 |                                                                
AGCCGAACTAAAGCGAAAAAACTGTTCAGCGTGGAAGATCAAATTCGTGCCACCGCGCATGTGGAATGCCGTAAAGATGCCGAAGTGATCGACGAAATCCCGATGGCGTATAAAGATATTGATGCGGTGA  >  minE/2664046‑2664175

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