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 2,143,681 G→A 21.7% intergenic (‑299/‑49) metY ← / → argG tRNA‑Met/argininosuccinate synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,143,6810GA21.7% 204.9 / 41.7 142intergenic (‑299/‑49)metY/argGtRNA‑Met/argininosuccinate synthetase
Reads supporting (aligned to +/- strand):  ref base G (36/75);  new base A (16/15);  total (52/90)
Fisher's exact test for biased strand distribution p-value = 5.94e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 150 total aligned reads displayed.

AACTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTATG  >  minE/2143613‑2143732
                                                                    |                                                   
aaCTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTgag                                                     >  1:1096083/1‑69 (MQ=255)
aaCTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTgag                                                     >  1:18733/1‑69 (MQ=255)
aaCTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTgag                                                     >  1:1861565/1‑69 (MQ=255)
aaCTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTgag                                                     >  1:2899392/1‑69 (MQ=255)
   tctTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGagag                                                   >  1:473694/1‑68 (MQ=255)
         tGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGa                                               <  1:3081016/66‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGa                                               <  1:1649173/65‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGa                                               <  1:2691666/65‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAAt                                            <  1:542313/68‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAAt                                            <  1:156341/68‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAAt                                            <  1:1108336/68‑1 (MQ=255)
          gTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAAt                                            <  1:481905/68‑1 (MQ=255)
           tctcCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATcc                                          >  1:1888154/1‑69 (MQ=255)
           tctcCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATcc                                          >  1:2710865/1‑69 (MQ=255)
           tctcCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATcc                                          >  1:1072136/1‑69 (MQ=255)
           tctcCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATcc                                          >  1:401436/1‑69 (MQ=255)
               cGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAGTTCAGTGAGAGCGGAAATCCAgg                                       >  1:705932/1‑68 (MQ=255)
               cGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAgg                                       >  1:1923931/1‑68 (MQ=255)
               cGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAg                                        >  1:2678721/1‑67 (MQ=255)
               cGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCAAgg                                       >  1:3392935/1‑68 (MQ=255)
                atcaaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCt                                     <  1:957147/66‑1 (MQ=255)
                atcaaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCt                                     <  1:548843/66‑1 (MQ=255)
                atcaaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCt                                     <  1:1041355/66‑1 (MQ=255)
                 aTAAGAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    <  1:43162/69‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAgg                                       <  1:330860/66‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAgg                                       <  1:2250453/66‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAgg                                       <  1:4274/66‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAgg                                       <  1:974485/66‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    <  1:941510/69‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    <  1:1252001/69‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    <  1:3155121/69‑1 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    >  1:238453/1‑69 (MQ=255)
                 aTAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtc                                    <  1:885052/69‑1 (MQ=255)
                   aaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcat                                  >  1:612885/1‑69 (MQ=255)
                   aaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcat                                  >  1:3431054/1‑69 (MQ=255)
                   aaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcat                                  >  1:2162432/1‑69 (MQ=255)
                   aaaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcat                                  >  1:477850/1‑69 (MQ=255)
                    aaaGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcat                                  <  1:2093247/68‑1 (MQ=255)
                      aGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtcatca                                <  1:1521488/68‑1 (MQ=255)
                           atTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGtt                          >  1:3023897/1‑69 (MQ=255)
                                     aaCTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCa                 <  1:1748133/68‑1 (MQ=255)
                                     aaCTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCa                 <  1:1041704/68‑1 (MQ=255)
                                     aaCTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCa                 <  1:59748/68‑1 (MQ=255)
                                     aaCTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCa                 <  1:16648/68‑1 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:2996512/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:1336480/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:3338513/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:3400762/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              <  1:488127/69‑1 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:2655465/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:2126545/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              >  1:3128060/1‑69 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              <  1:2480852/69‑1 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              <  1:64997/69‑1 (MQ=255)
                                       cTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAgg               >  1:1692597/1‑68 (MQ=255)
                                          atttatttTGCATAAATATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAggg              <  1:229067/66‑1 (MQ=255)
                                            ttatttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGgtgt           <  1:3241535/67‑1 (MQ=255)
                                            ttatttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGgtgt           <  1:1227934/67‑1 (MQ=255)
                                            ttatttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGgtgt           <  1:2665128/67‑1 (MQ=255)
                                            ttatttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGgtgt           <  1:1999375/67‑1 (MQ=255)
                                             tatttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGgtgt           <  1:2104773/66‑1 (MQ=255)
                                              atttTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAt        >  1:2257504/1‑68 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:349670/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1989189/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1423214/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1551278/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1602484/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1669844/68‑1 (MQ=255)
                                                tttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:831653/68‑1 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtca                                   >  1:2961848/1‑38 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtca                                   >  1:1460436/1‑38 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtca                                   >  1:2542925/1‑38 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCtca                                   >  1:1036377/1‑38 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:989516/67‑1 (MQ=255)
                                                 ttGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTAttt      <  1:1189217/67‑1 (MQ=255)
                                                   gCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:2332357/68‑1 (MQ=255)
                                                    cATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:498418/67‑1 (MQ=255)
                                                    cATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTATg  <  1:85844/68‑1 (MQ=255)
                                                    cATAAAAATTCAGTGAGAGCGGAAATCCAGGCGCATCATCAGTTAATTAAGCAGGGTGTTATTTTATg  <  1:70875/68‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2360149/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:978267/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:1197479/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:972012/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:1624916/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:1904523/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2302105/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:869216/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:2445342/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2499011/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2502840/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2538201/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:2668143/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:3198246/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:475175/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   >  1:3434647/1‑64 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTAt   <  1:360124/64‑1 (MQ=255)
                                                       aaaaaTTCAGTGAAAGCAGAAATCCACGCtcatcat                               >  1:2322648/1‑36 (MQ=37)
                                                       aaaaaTTCAGAGAAAGCAGAAATCCAGGCTCATCATCAGttaattaa                    >  1:560597/1‑47 (MQ=37)
                                                        aaaaTTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGtt                          <  1:402657/40‑1 (MQ=255)
                                                        aaaaTTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGtt                          <  1:3145104/40‑1 (MQ=255)
                                                                    |                                                   
AACTCTTCCTGTCTCCGATAAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGAGAGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTTATG  >  minE/2143613‑2143732

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