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 2,786,713 G→A 30.2% T39T (ACC→ACT)  yjbD ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,786,7130GA30.2% 110.7 / 51.9 112T39T (ACC→ACT) yjbDconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (53/25);  new base A (13/21);  total (66/46)
Fisher's exact test for biased strand distribution p-value = 6.13e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

Only 100 of 120 total aligned reads displayed.

TTCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACG  >  minE/2786654‑2786781
                                                           |                                                                    
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:2620278/67‑1 (MQ=255)
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:2030780/67‑1 (MQ=255)
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:430105/67‑1 (MQ=255)
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:2258091/67‑1 (MQ=255)
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:330119/67‑1 (MQ=255)
ttCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:3239677/67‑1 (MQ=255)
      tCAGCCTCACGCTCGAGCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:1205527/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:3288455/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:2577377/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:177063/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:2609843/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:2637073/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:1851463/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:2285110/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:144723/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:3363329/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:638618/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:1081167/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:866966/68‑1 (MQ=255)
      tCAGCCTCACGCTCGACCATTAATTTATCGATGTACTCTTTCTTAATGCTGTTAGTTTCGGAGTTGGt                                                        <  1:2063094/68‑1 (MQ=255)
      tCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTTGTc                                                       <  1:2922872/69‑1 (MQ=255)
      tCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTc                                                       <  1:191166/69‑1 (MQ=255)
      tCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTc                                                       <  1:1680173/69‑1 (MQ=255)
      tCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTc                                                       <  1:786486/69‑1 (MQ=255)
         gCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCaa                                                     <  1:2734119/68‑1 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCgg                                                               <  1:2898112/50‑1 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCa                                                      >  1:152874/1‑59 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAcc                                            >  1:771397/1‑69 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAcc                                            >  1:879513/1‑69 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:2463072/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:1022282/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:381293/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:2190377/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:2148041/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:1255758/1‑68 (MQ=255)
                 cTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGAc                                             >  1:1826796/1‑68 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTc                                                       >  1:2106693/1‑48 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAAt                                                    >  1:1077845/1‑51 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAAt                                                    >  1:128388/1‑51 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAAt                                                    >  1:3008427/1‑51 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAAt                                                    >  1:481390/1‑51 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGCCCATGCGCAATc                                  >  1:1381830/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAAta                                  >  1:3432726/1‑68 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:2299591/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:105854/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:773937/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:811783/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:542014/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:2692867/1‑69 (MQ=255)
                           aaTTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATc                                  >  1:1778351/1‑69 (MQ=255)
                               tATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCcgcg                              >  1:2855529/1‑69 (MQ=255)
                               tATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCcgcg                              >  1:36835/1‑69 (MQ=255)
                               tATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCcgcg                              >  1:218993/1‑69 (MQ=255)
                                     tGTAATCTTTGTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:2352672/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         <  1:1290395/68‑1 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:3181158/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:70157/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:1382270/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:2856901/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         <  1:2778763/68‑1 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:1608930/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         >  1:2153353/1‑68 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGa                         <  1:640521/68‑1 (MQ=255)
                                     tGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCAGCGCCCg                          >  1:3280606/1‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCTCCCGATcc                      >  1:1940131/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:3381805/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:434234/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:445843/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:1395844/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:3175990/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:1993453/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:909716/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:2322321/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTTTCGGAGTTGGTCAGTACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:1152617/2‑67 (MQ=255)
                                         ctctttcttAATGCTGTTAGTATCGGAGTTGGTCAGTa                                                   >  1:2418630/2‑38 (MQ=255)
                                         aTCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATAcgc                                                >  1:296757/1‑41 (MQ=255)
                                         aTCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:1165207/1‑67 (MQ=255)
                                         aTCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:806970/1‑67 (MQ=255)
                                         aTCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATcc                      >  1:1176850/1‑67 (MQ=255)
                                           ctttcttAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCTCGCCCGATCcagc                   <  1:3251103/68‑1 (MQ=255)
                                                ttAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:955220/65‑1 (MQ=255)
                                                ttAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:3420285/65‑1 (MQ=255)
                                                ttAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:652237/65‑1 (MQ=255)
                                                ttAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:304037/65‑1 (MQ=255)
                                                 tAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:1653501/64‑1 (MQ=255)
                                                 tAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCcagcag                 <  1:656372/64‑1 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTaa         >  1:3218793/1‑67 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAg        >  1:1518706/1‑68 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAg        >  1:173700/1‑68 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAg        >  1:2401020/1‑68 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAg        >  1:1864634/1‑68 (MQ=255)
                                                      cTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAg        >  1:205323/1‑68 (MQ=255)
                                                      cTGTTGGATTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGtttt           >  1:2534429/1‑65 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:3347557/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:293372/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:1478813/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:2689302/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:2331473/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:1006250/1‑69 (MQ=255)
                                                           ggTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACg  >  1:90779/1‑69 (MQ=255)
                                                           |                                                                    
TTCGCTTCAGCCTCACGCTCAACCATTAATTTATCGATGTAATCTTTCTTAATGCTGTTGGTTTCGGAGTTGGTCAATACGCGACCATGCGCAATCCGCGCCCGATCCAGCAGTGTTTTAAGTTCACG  >  minE/2786654‑2786781

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