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 774,641 T→C 44.1% T88T (ACT→ACC)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE774,6410TC44.1% 20.2 / 83.6 102T88T (ACT→ACC) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base T (17/40);  new base C (17/28);  total (34/68)
Fisher's exact test for biased strand distribution p-value = 4.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

TGGAAATTTACACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTG  >  minE/774574‑774702
                                                                   |                                                             
tggaAATTTACACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAActc                                                              >  1:1764923/1‑69 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:840989/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:2271234/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:2755233/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:304676/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:391909/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:451381/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTg                                               <  1:1034891/69‑1 (MQ=255)
               gTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTAGATCTGATTCGTg                                               <  1:1090528/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:2072356/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:1158297/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:380916/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:2430258/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:3271522/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:729760/69‑1 (MQ=255)
                 gAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGaa                                             <  1:3042623/69‑1 (MQ=255)
                       tCCACACAGGTTTATGTTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATcgc                                       <  1:1671207/69‑1 (MQ=255)
                       tCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATcgc                                       <  1:2777298/69‑1 (MQ=255)
                                      ggTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAgg                         <  1:2291998/68‑1 (MQ=255)
                                      ggTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAgg                         <  1:566532/68‑1 (MQ=255)
                                      ggTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAgg                         <  1:1341437/68‑1 (MQ=255)
                                      ggTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGGTGCCATTAAAgg                         <  1:203942/68‑1 (MQ=255)
                                        tCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATcgc                                       <  1:152679/52‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:331201/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:560348/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:445245/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2081878/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2214392/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1006540/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2275256/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:3331348/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2409008/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:487661/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:3228515/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2436657/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2446126/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:3195971/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2516400/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:2706837/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:31685/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1006441/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1141993/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1171120/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:118791/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1258607/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1715895/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1690069/61‑1 (MQ=255)
                                         cAGGACGTCTGGTTGCCTGCTGAAACCCTTGATCAGATTCGTGAATATCGCGTTGCCATTa                             <  1:2015490/61‑1 (MQ=255)
                                          aGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTTAATATCGCGTTGCCATTa                             <  1:1227985/60‑1 (MQ=255)
                                          aGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1267898/60‑1 (MQ=255)
                                          aGGACGTCTGGTTGCCTGCTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCATTa                             <  1:1411639/60‑1 (MQ=255)
                                            gACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCt                   <  1:2206321/68‑1 (MQ=255)
                                            gACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCt                   <  1:888564/68‑1 (MQ=255)
                                            gACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCt                   <  1:598373/68‑1 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTcc                      >  1:3021391/1‑64 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCt                   <  1:3404054/67‑1 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:2678189/1‑68 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:1553517/1‑68 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:52270/1‑68 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:2285144/1‑68 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:3424263/1‑68 (MQ=255)
                                             aCGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTg                  >  1:326617/1‑68 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:2327733/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:961841/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:834420/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:64856/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:1032315/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:1145470/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:1848264/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:3261122/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:1304672/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:180815/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGAc                <  1:3012652/69‑1 (MQ=255)
                                              cGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTAAc                <  1:155597/69‑1 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:147702/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2586611/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:200609/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:750181/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:1009225/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2001772/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2734333/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2761150/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:518299/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2462275/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:1459590/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:1171628/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:2479924/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:1241709/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTGCCAtt                              >  1:1837770/1‑46 (MQ=255)
                                                       gcctgcTGAAACCCTTGATCTGATTCGTGAATATCGCGTTCCCAtt                              >  1:609341/1‑46 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTTCCATTAAAGGTCCGCt                   >  1:2643773/1‑52 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTtggtg  >  1:3234860/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:3303811/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:653321/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:1656120/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:3195917/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:1108973/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:2004587/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggtg  >  1:1143338/1‑69 (MQ=255)
                                                            ctgAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTtggt   >  1:415129/1‑68 (MQ=255)
                                                                   |                                                             
TGGAAATTTACACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTG  >  minE/774574‑774702

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