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 2,031,571 A→G 59.4% D237D (GAT→GAC)  cpdA ← cyclic 3',5'‑adenosine monophosphate phosphodiesterase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,031,5710AG59.4% 38.1 / 59.0 86D237D (GAT→GAC) cpdAcyclic 3',5'‑adenosine monophosphate phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base A (17/18);  new base G (22/29);  total (39/47)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACCTCGGTGGTCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAGGCGGC  >  minE/2031507‑2031638
                                                                |                                                                   
gCACCTCGGTGGTCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCa                                                                 >  1:972330/1‑69 (MQ=255)
gCACCTCGGTGGTCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCa                                                                 >  1:1181003/1‑69 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCTATGGTGTCCAGCGTAAAGtt                                                       <  1:2151016/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:1635680/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:158114/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:602069/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:1502890/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:2677579/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:938136/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:2969761/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:477037/69‑1 (MQ=255)
          ggtCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAGtt                                                       <  1:2580030/69‑1 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:634160/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:3274174/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:1977514/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:746368/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:18998/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:3341595/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2126238/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:213727/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:410791/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:349522/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2419338/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:661503/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2611925/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:1811138/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:752415/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:1583363/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:3258462/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2702761/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2712023/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:1374368/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:973605/1‑52 (MQ=255)
                         aGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTGTCCAGCGTAAAg                                                         >  1:2828053/1‑52 (MQ=255)
                           cATGTAACTCTAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:131271/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2052716/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2533831/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2861100/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:1042988/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:1066567/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2050287/68‑1 (MQ=255)
                           cATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2387141/68‑1 (MQ=255)
                            aTGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTa                                       <  1:2334101/67‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCTCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:1391765/69‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:391528/69‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:1921702/69‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:1325663/69‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:854737/69‑1 (MQ=255)
                             tGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAAc                                    <  1:1493668/69‑1 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTaaa                                                          <  1:312297/45‑1 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTaaa                                                          <  1:3072354/45‑1 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTaaa                                                          <  1:1423187/45‑1 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:3155201/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:3105886/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:707393/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:2632713/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:3376192/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:2775761/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:1642368/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:1542318/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:1849149/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:2049450/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:2325333/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:241112/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:2556940/1‑69 (MQ=255)
                               tAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTg                                  >  1:1017379/1‑69 (MQ=255)
                                            cGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGAc                     >  1:2626624/1‑69 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2655059/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:1169891/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:1889881/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2911755/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2055198/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:1490288/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2173316/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2210564/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2226240/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2738161/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:349343/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:305473/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:3349640/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2717331/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:3328728/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2568227/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:941262/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:3186463/68‑1 (MQ=255)
                                              ccAGCCGGGCGCGATGGTGTCCAGCGTAAAGTTAGAACAGTGCGGCTTAAACTGCACACAGGTCGACg                    <  1:2643034/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:1171559/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:98181/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:1777807/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:477445/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:32399/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:2768861/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:2830018/68‑1 (MQ=255)
                                                                aTCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAggcggc  <  1:2773055/68‑1 (MQ=255)
                                                                |                                                                   
GCACCTCGGTGGTCAGCGTGCCATCAGCATGTAACTCGAGAGTACGCCAGCCGGGCGCGATGGTATCCAGCGTAAAGTTGGAACAGTGCGGCTTAAACTGCACACAGGTCGACGGCGTTGCCAGCAGGCGGC  >  minE/2031507‑2031638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A