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 1,469,318 C→T 38.0% V802I (GTT→ATT)  yfaL ← adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,469,3180CT38.0% 62.7 / 66.6 105V802I (GTT→ATT) yfaLadhesin
Reads supporting (aligned to +/- strand):  ref base C (53/12);  new base T (24/16);  total (77/28)
Fisher's exact test for biased strand distribution p-value = 2.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.58e-01

Only 100 of 107 total aligned reads displayed.

GTACCGCCGCCGGTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGT  >  minE/1469251‑1469384
                                                                   |                                                                  
gTACCGCCGCCTGTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAAc                                                                    <  1:2029362/68‑1 (MQ=255)
            gTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTa                                                       <  1:1728674/69‑1 (MQ=255)
            gTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTa                                                       <  1:147740/69‑1 (MQ=255)
            gTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTa                                                       <  1:199413/69‑1 (MQ=255)
            gTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTa                                                       <  1:440758/69‑1 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1741290/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1737471/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:3357081/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1770644/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1354664/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:2085891/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1269050/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:632555/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:1152919/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:2497124/1‑67 (MQ=255)
                 aTCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTg                                                    >  1:2401881/1‑67 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2855555/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2093409/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2142050/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2595091/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:3270995/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:1868504/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:1742543/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2580528/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:3277947/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:572540/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:1119345/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:874936/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:1342956/69‑1 (MQ=255)
                        tttACCGTCAGCGTGTCGCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:150357/69‑1 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAAc                                                                    >  1:2756938/1‑42 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:3274859/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:788827/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:2699852/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:1210436/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:53320/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:3002093/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:1917175/1‑53 (MQ=255)
                          tACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACg                                                         >  1:352818/1‑53 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGc                                          <  1:1282063/55‑1 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGc                                          <  1:241612/55‑1 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGc                                          <  1:1972378/55‑1 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGc                                          <  1:1122047/55‑1 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGc                                          <  1:2279294/55‑1 (MQ=255)
                                       tCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACg                            >  1:170610/1‑69 (MQ=255)
                                         gCCAGCGACGCCATTTTGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:2197311/52‑1 (MQ=255)
                                         gCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGt                           >  1:2720249/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:954543/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:3399137/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:3083243/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2730763/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:404590/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2796146/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2233977/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2208297/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2147302/1‑68 (MQ=255)
                                               gACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGaaa                     >  1:2108588/1‑68 (MQ=255)
                                                     aTTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATaa                >  1:3066939/1‑67 (MQ=255)
                                                     aTTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATaa                >  1:2933963/1‑67 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGGCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3287042/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:308755/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3214342/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3111161/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2395378/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1946990/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1768235/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3378241/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3408627/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1479385/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1447776/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1279995/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1235874/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:871504/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:1049273/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2294883/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2380202/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2477296/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:23175/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:196955/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2672316/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:3002637/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2070869/1‑69 (MQ=255)
                                                      ttttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTCGGAAAGATAAGTc             >  1:2816694/1‑69 (MQ=255)
                                                        ttGCAGGCTAATCGCACCGGACGTATTGGTCAGATTg                                           <  1:1501519/37‑1 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:1430092/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:1166234/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:689768/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:2348996/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:2944453/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:226403/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:3353503/1‑69 (MQ=255)
                                                                tAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAg   >  1:3331645/1‑69 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGTCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:1995195/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTTTCAGt  >  1:713783/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:37676/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:1948874/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:1229143/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:1731026/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:2454142/1‑68 (MQ=255)
                                                                  aCCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGt  >  1:114413/1‑68 (MQ=255)
                                                                   |                                                                  
GTACCGCCGCCGGTATAATCACCGTTTACCGTCAGCGTATCGCCAGCGACGCCATTTTGCAGGCTAACCGCACCGGACGTATTGGTCAGATTGCCATTAACCGTCACGTTGGAAAGATAAGTCAGGCTGTCAGT  >  minE/1469251‑1469384

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