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 827,457 G→A 27.2% L18L (CTG→TTG)  narL ← DNA‑binding response regulator in two‑component regulatory system with NarX (or NarQ)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE827,4570GA27.2% 121.4 / 41.9 106L18L (CTG→TTG) narLDNA‑binding response regulator in two‑component regulatory system with NarX (or NarQ)
Reads supporting (aligned to +/- strand):  ref base G (60/17);  new base A (20/9);  total (80/26)
Fisher's exact test for biased strand distribution p-value = 4.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

Only 100 of 110 total aligned reads displayed.

ACTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAC  >  minE/827392‑827524
                                                                 |                                                                   
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:386584/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:3237033/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:1983681/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:1846995/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:2791406/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:3309605/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:3420607/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:545884/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:692315/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:88277/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:2533550/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:1134263/1‑69 (MQ=255)
aCTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCAt                                                                  >  1:2456481/1‑69 (MQ=255)
      ttCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTg                                                            <  1:258431/69‑1 (MQ=255)
      ttCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTg                                                            <  1:3210909/69‑1 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:2329561/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:230720/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:1952738/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:2289715/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:2775644/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:2745925/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:2688422/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:3063105/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:3233800/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:3251301/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:1271616/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:3288826/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:905089/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:708075/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:642916/1‑56 (MQ=255)
               cACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:3244063/1‑56 (MQ=255)
               cACGGTGATATCTCGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAACATCg                                                                >  1:1068647/1‑56 (MQ=255)
                     gATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGGAGCATCGGGTGATCGTCAATcagcag                                             >  1:2252272/1‑69 (MQ=255)
                     gATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCTGGTGATCGTCAATca                                                 >  1:1605340/1‑65 (MQ=255)
                     gATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATcagcag                                             >  1:1704640/1‑69 (MQ=255)
                         tCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGAt                                          <  1:1670139/68‑1 (MQ=255)
                                  aTACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGt                                <  1:2101726/69‑1 (MQ=255)
                                  aTACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGt                                <  1:3260955/69‑1 (MQ=255)
                                  aTACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGt                                <  1:1054500/69‑1 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCg                                  >  1:3050735/1‑64 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:3009600/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:934262/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2657766/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2616711/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:957698/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2450906/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:1934856/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:220500/1‑68 (MQ=255)
                                     cTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2013008/1‑68 (MQ=255)
                                     cTGATAAGCTGCTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:833203/1‑68 (MQ=255)
                                     cTGATAAGCTGCTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:800775/1‑68 (MQ=255)
                                     cTGATAAGCTGCTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2711704/1‑68 (MQ=255)
                                     cTGATAAGCTGCTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTc                              >  1:2277988/1‑68 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:120118/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:2455526/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:1273965/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:743193/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:624582/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:1691343/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:3101702/68‑1 (MQ=255)
                                          aaGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:3009845/68‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAtt                        >  1:3094722/1‑68 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAtt                        >  1:468257/1‑68 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTa                       >  1:3029749/1‑69 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTa                       >  1:2022063/1‑69 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTa                       >  1:291446/1‑69 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTa                       >  1:3360819/1‑69 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:2412577/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:1340392/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:2619668/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:2638727/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:200091/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:136125/69‑1 (MQ=255)
                                           aGCTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:1704664/69‑1 (MQ=255)
                                             cTGTTTTACGCCAGTTCGCAACATCGGGTGATCGTCGATCAGCAGGATAGTAGCCGGTTCCTGATTa                       <  1:2971500/67‑1 (MQ=255)
                                                 tttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGAt                         <  1:3100282/61‑1 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATcagcag                                             >  1:1923831/1‑40 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACt                     >  1:293327/1‑64 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACt                     >  1:323793/1‑64 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACt                     >  1:3072009/1‑64 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACt                     >  1:1414465/1‑64 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATg                 >  1:2763285/1‑68 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATg                 >  1:1281267/1‑68 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATg                 >  1:241066/1‑68 (MQ=255)
                                                  ttACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATg                 >  1:514821/1‑68 (MQ=255)
                                                  ttACGACAGTTCGCAGCATCGGGTGATCGTCAATAAGCAGGATAGTAGCCGGTTCCTGATTACTCAta                 >  1:1533431/1‑67 (MQ=255)
                                                         aGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTAtctc         <  1:2597821/69‑1 (MQ=255)
                                                          gTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTAtctc         <  1:1698408/68‑1 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:3246314/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:2384377/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:1961586/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:199066/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:1564815/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:2359976/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:1954992/1‑69 (MQ=255)
                                                             cGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTg     >  1:2203253/1‑69 (MQ=255)
                                                                agcaTCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAc  <  1:473866/69‑1 (MQ=255)
                                                                agcaTCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAc  <  1:561992/69‑1 (MQ=255)
                                                                agcaTCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAc  <  1:1388436/69‑1 (MQ=255)
                                                                agcaTCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAc  <  1:339805/69‑1 (MQ=255)
                                                                 |                                                                   
ACTCGCTTCGCCAACCACGGTGATATCTGGTGCCATACTGATAAGCTGTTTTACGCCAGTTCGCAGCATCGGGTGATCGTCAATCAGCAGGATAGTAGCCGGTTCCTGATTACTCATGGGTATCTCCTTGGAC  >  minE/827392‑827524

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