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 2,642,719 C→A 28.1% S117S (TCC→TCA)  gntR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,642,7190CA28.1% 150.2 / 53.5 103S117S (TCC→TCA) gntRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (52/22);  new base A (19/10);  total (71/32)
Fisher's exact test for biased strand distribution p-value = 6.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.85e-01

Only 100 of 103 total aligned reads displayed.

AGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAGATGATTGA  >  minE/2642652‑2642784
                                                                   |                                                                 
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:1008314/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:3295490/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:1489990/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:1003979/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:1267906/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:2766302/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:1046324/69‑1 (MQ=255)
aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                                                  <  1:869301/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCGATGCTCTCATgg                                                                <  1:908837/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:2954329/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:1442107/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:1437801/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:2500203/69‑1 (MQ=255)
  aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:498392/69‑1 (MQ=255)
   ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                                                <  1:137622/68‑1 (MQ=255)
   ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                                               <  1:2730021/69‑1 (MQ=255)
   ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                                               <  1:3274113/69‑1 (MQ=255)
   ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                                               <  1:2911980/69‑1 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:203879/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2945047/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2252848/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2500819/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1993772/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2600194/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:265512/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:3211087/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1892637/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1850644/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1806915/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1729773/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2822448/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1732831/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1614683/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1069082/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1408603/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:147628/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:3335722/1‑69 (MQ=255)
        cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:1201063/1‑69 (MQ=255)
        cTGGAGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                                          >  1:2079242/1‑69 (MQ=255)
              cACTACGGTTATAAACTGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                                                    <  1:3185965/69‑1 (MQ=255)
              cACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                                                    <  1:3240559/69‑1 (MQ=255)
              cACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                                                    <  1:3236611/69‑1 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:2384644/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:509463/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1293481/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:414058/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:2600287/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:2628744/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1144153/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1576353/1‑69 (MQ=255)
                  aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGATCTCCTGGAATATCGACGGCCTGa                                                >  1:1572591/1‑69 (MQ=255)
                                  aaTGGCGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:2072095/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCTAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:2855905/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTGTCATGGAATATCGACGGCCTGATCCTCActg                                       >  1:2934031/1‑60 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACgg                                                     >  1:2164016/1‑48 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:64977/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1091167/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1300651/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:2890563/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:2146787/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1333670/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:358722/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1982351/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1964037/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1541996/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1811745/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa                                 >  1:1675452/1‑68 (MQ=255)
                                  aaTGGAGCAAGAACGCCTCGAAACAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGa                                      >  1:855479/1‑63 (MQ=255)
                                    tGGAGGAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1321937/1‑51 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:2959998/1‑51 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:2013043/1‑51 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                <  1:3333409/51‑1 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                <  1:2878295/51‑1 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                <  1:1681309/51‑1 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1110091/1‑51 (MQ=255)
                                    tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                >  1:1789164/1‑51 (MQ=255)
                                      gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac                            >  1:3284195/1‑69 (MQ=255)
                                      gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac                            >  1:489796/1‑69 (MQ=255)
                                      gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac                            >  1:1748849/1‑69 (MQ=255)
                                      gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac                            >  1:1988492/1‑69 (MQ=255)
                                        gCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCacac                          >  1:1441271/1‑69 (MQ=255)
                                                gCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                                                <  1:1040269/39‑1 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1896992/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1943798/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1955598/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1719753/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:2144534/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1217126/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1431330/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatga      >  1:1330355/1‑69 (MQ=255)
                                                            tGCTCTCCTGGAATATCGACGGCCTGATCCTAACCGAACGTACCCACACGCCGCGCACCTTAAAgatg       >  1:1465746/1‑68 (MQ=255)
                                                              ctctCCTGGAATATCGACGGTCTGATCCTCACCGAACGTAcc                               <  1:559880/42‑1 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTAcc                               <  1:946785/42‑1 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTAcc                               <  1:1009752/42‑1 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTAcc                               <  1:147166/42‑1 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTAcc                               <  1:2453976/42‑1 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatgat     >  1:3315009/1‑68 (MQ=255)
                                                              ctctCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAgatgat     >  1:267875/1‑68 (MQ=255)
                                                                ctcCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAGATGATTGa  <  1:334896/69‑1 (MQ=255)
                                                                 tcCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAGATGATTGa  <  1:1685119/68‑1 (MQ=255)
                                                                   |                                                                 
AGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACACGCCGCGCACCTTAAAGATGATTGA  >  minE/2642652‑2642784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A