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 2,722,373 A→G 59.4% intergenic (‑122/‑180) crp ← / → yhfA DNA‑binding transcriptional dual regulator/conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,722,3730AG59.4% 50.1 / 79.4 113intergenic (‑122/‑180)crp/yhfADNA‑binding transcriptional dual regulator/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/32);  new base G (45/22);  total (59/54)
Fisher's exact test for biased strand distribution p-value = 1.38e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-01

Only 100 of 121 total aligned reads displayed.

TCTGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGTTTTAG  >  minE/2722305‑2722431
                                                                    |                                                          
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:2810844/1‑69 (MQ=255)
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:2850890/1‑69 (MQ=255)
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:3374350/1‑69 (MQ=255)
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:3378834/1‑69 (MQ=255)
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:1394558/1‑69 (MQ=255)
tctGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGa                                                            >  1:1445103/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:444091/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:3115376/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:2472006/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:327722/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:885091/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:148920/1‑69 (MQ=255)
  tGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACg                                                          >  1:410289/1‑69 (MQ=255)
             aaTATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATa                                               <  1:1948199/69‑1 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATa                                               >  1:3105587/1‑68 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:3337952/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:3364712/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:2369517/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:1966156/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:1153872/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:2047663/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:814515/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:3147659/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:2847791/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:159667/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:2746341/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:2749601/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATAc                                              >  1:1432049/1‑69 (MQ=255)
              atatGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGGAGTCCTTTGCATAc                                              >  1:2550905/1‑69 (MQ=255)
                     tCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAg                                        <  1:1848091/68‑1 (MQ=255)
                     tCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAg                                        <  1:841707/68‑1 (MQ=255)
                     tCCCGCCACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAg                                        <  1:644264/68‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:359536/69‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:2628775/69‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:574750/69‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:126798/69‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:1793079/69‑1 (MQ=255)
                          cTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:3379051/69‑1 (MQ=255)
                            aCCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCaa                                <  1:520617/69‑1 (MQ=255)
                            aCCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCaa                                <  1:1124792/69‑1 (MQ=255)
                            aCCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCaa                                <  1:1529683/69‑1 (MQ=255)
                             ccTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCaa                                <  1:791565/68‑1 (MQ=255)
                                 ggAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:1760037/62‑1 (MQ=255)
                                   aaGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTAtt                          <  1:1788556/68‑1 (MQ=255)
                                   aaGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTAtt                          <  1:3414451/68‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:399689/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:3713/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2987332/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:3397777/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:358576/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:251033/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:1564220/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:1663509/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2649550/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:1948900/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2031030/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2056944/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2331643/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:935127/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:2484715/69‑1 (MQ=255)
                                     ggggCTATCAACTGTACTGCACGGTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACt                       <  1:710024/69‑1 (MQ=255)
                                            tCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATc                                  <  1:344289/51‑1 (MQ=255)
                                              aaCTGTACTGCACGGTAATGTGACGTCCTTTGCATa                                               >  1:45340/1‑36 (MQ=255)
                                              aaCTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATc               >  1:3159764/1‑68 (MQ=255)
                                              aaCTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATc               >  1:2563186/1‑68 (MQ=255)
                                              aaCTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATc               >  1:1085225/1‑68 (MQ=255)
                                                cTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCt             <  1:1197961/68‑1 (MQ=255)
                                                cTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCt             <  1:2021927/68‑1 (MQ=255)
                                                cTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCt             <  1:2831998/68‑1 (MQ=255)
                                                cTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCt             <  1:2773581/68‑1 (MQ=255)
                                                  gTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGAc          >  1:2922184/1‑69 (MQ=255)
                                                  gTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGAc          >  1:3357231/1‑69 (MQ=255)
                                                     cTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGt       <  1:202315/69‑1 (MQ=255)
                                                     cTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGt       <  1:1598348/69‑1 (MQ=255)
                                                      tGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGt       <  1:1323737/68‑1 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTa   >  1:956484/1‑67 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTa   >  1:1740807/1‑67 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTa   >  1:2599275/1‑67 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:971212/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:748165/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2752711/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:606949/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:624306/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:630320/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:3393633/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:3179071/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:3157599/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:3092179/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2883145/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2786394/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2507093/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2332169/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2161062/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:2157312/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:1725968/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:1560250/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:151340/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:1321802/1‑68 (MQ=255)
                                                           ggTAATGTGGCGTCCTTTGCATACATGCAGTACATCAATATATTACTGTAGCATCCTGACTGTTTTAg  >  1:1146762/1‑68 (MQ=255)
                                                               aTGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGt       <  1:1093741/59‑1 (MQ=255)
                                                                    |                                                          
TCTGGATTGCCGAAATATGCTTCCCGCTACCTGGGAAGGGGCTATCAACTGTACTGCACGGTAATGTGACGTCCTTTGCATACATGCAGTACATCAATGTATTACTGTAGCATCCTGACTGTTTTAG  >  minE/2722305‑2722431

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