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 1,553,378 C→G 52.7% intergenic (‑129/‑89) dsdC ← / → dsdX DNA‑binding transcriptional dual regulator/predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,553,3780CG52.7% 16.4 / 180.2 146intergenic (‑129/‑89)dsdC/dsdXDNA‑binding transcriptional dual regulator/predicted transporter
Reads supporting (aligned to +/- strand):  ref base C (59/10);  new base G (16/61);  total (75/71)
Fisher's exact test for biased strand distribution p-value = 9.34e-16
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

Only 100 of 146 total aligned reads displayed.

AAAGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAATA  >  minE/1553314‑1553435
                                                                |                                                         
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:956443/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:2100861/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:2801895/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:2803763/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:3250446/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:3260198/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:398466/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:47763/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:636096/69‑1 (MQ=255)
aaaGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:1227426/69‑1 (MQ=255)
             tctcAATTCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCa                                                       <  1:1492768/56‑1 (MQ=255)
             tctcAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCaaa                                          >  1:2394433/1‑69 (MQ=255)
               tcAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCaaa                                          >  1:2121386/1‑67 (MQ=255)
               tcAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCaaa                                          >  1:2521740/1‑67 (MQ=255)
               tcAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAAt                                         >  1:2389676/1‑68 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:681269/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:2444326/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:2017053/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:2504551/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1929046/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1901096/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:2545400/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:2693751/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:920906/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:809922/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:3034608/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:3146542/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1112508/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:404660/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1415862/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1369182/66‑1 (MQ=255)
                   ttCACCTTCATTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAAttt                                       <  1:1292661/66‑1 (MQ=255)
                     cACCTTCATTTTTAGACGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCg                                  <  1:799680/69‑1 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:3122646/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:75954/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:741435/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:2433065/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:96495/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:600120/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:2264939/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:1035314/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:1120073/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:1134599/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:1211483/1‑69 (MQ=255)
                            aTTTTTAGATGTAAATCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           >  1:208868/1‑69 (MQ=255)
                             tttttAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           <  1:2082301/68‑1 (MQ=255)
                              ttttAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCa                           <  1:1519486/67‑1 (MQ=255)
                               tttAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAg                          <  1:1405881/67‑1 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAAt                                         >  1:3010484/1‑44 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGc                     >  1:2375993/1‑64 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttgt                >  1:1072319/1‑69 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttgt                >  1:2363570/1‑69 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttgt                >  1:612234/1‑69 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttgt                >  1:1457208/1‑69 (MQ=255)
                                       tAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttgt                >  1:166557/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAAtttt                                      >  1:1008888/1‑45 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCg                                  >  1:2152268/1‑49 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCg                                  >  1:2817367/1‑49 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCg                                  >  1:172752/1‑49 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCg                                  >  1:25838/1‑49 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCgttg                 >  1:1469433/1‑66 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:3349662/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:3385586/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:3285128/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:370475/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:422838/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:314651/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:3111759/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:3051062/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:1792528/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:2007400/1‑69 (MQ=255)
                                         aaTCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttt              >  1:1770764/1‑69 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:1977095/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:2357050/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:1807624/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:2722322/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:3273330/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:1039773/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:3224158/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:3176663/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:3344485/69‑1 (MQ=255)
                                           tCACTCCCTTGATGCAATTTAGCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:2173326/69‑1 (MQ=255)
                                            cACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGtttttt           >  1:1162339/1‑69 (MQ=255)
                                                ccATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGt        >  1:2167439/1‑68 (MQ=255)
                                                ccATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGt        >  1:806068/1‑68 (MQ=255)
                                                 cATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTcc      >  1:1261157/1‑69 (MQ=255)
                                                 cATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTcc      >  1:570513/1‑69 (MQ=255)
                                                 cATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTcc      >  1:2408842/1‑69 (MQ=255)
                                                 cATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTcc      >  1:479131/1‑69 (MQ=255)
                                                 cATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTcc      >  1:924637/1‑69 (MQ=255)
                                                    tGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   <  1:1720436/69‑1 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:890510/1‑68 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:2773012/1‑68 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:1298671/1‑68 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:591120/1‑68 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:2614655/1‑68 (MQ=255)
                                                     gATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAat   >  1:167471/1‑68 (MQ=255)
                                                      aTGCAATTTAGCTCTTGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGttttt            <  1:1764027/58‑1 (MQ=255)
                                                              tACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAata  >  1:651137/1‑60 (MQ=255)
                                                              tACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAata  >  1:2243405/1‑60 (MQ=255)
                                                                |                                                         
AAAGTGAACCATATCTCAATTCACCTTCATTTTTAGATGTAAATCACTCCATTGATGCAATTTACCTCATGTGAAAGGCAAATTTTATCGTTTGTCAGCCTGCGTTGTTTTTTTGTCCAATA  >  minE/1553314‑1553435

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