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 2,011,421 A→G 35.4% T255T (ACA→ACG)  yghZ → aldo‑keto reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,011,4210AG35.4% 70.6 / 65.4 110T255T (ACA→ACG) yghZaldo‑keto reductase
Reads supporting (aligned to +/- strand):  ref base A (57/14);  new base G (30/9);  total (87/23)
Fisher's exact test for biased strand distribution p-value = 8.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-03

Only 100 of 111 total aligned reads displayed.

TCTCAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATGGCACAGCAG  >  minE/2011358‑2011484
                                                               |                                                               
tctcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:2895090/69‑1 (MQ=255)
tctcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:1222437/69‑1 (MQ=255)
tctcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:2708919/69‑1 (MQ=255)
tctcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:2367957/69‑1 (MQ=255)
 ctcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:1660055/68‑1 (MQ=255)
  tcAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGTGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:275719/67‑1 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGaa                                                            <  1:2145373/59‑1 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTa                                                    >  1:256746/1‑67 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTAc                                                   >  1:633157/1‑68 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTAc                                                   >  1:2091011/1‑68 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTAc                                                   >  1:1577463/1‑68 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTAc                                                   >  1:2607857/1‑68 (MQ=255)
          aTTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTAc                                                   >  1:3264314/1‑68 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:940175/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:2615842/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:2695168/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:425788/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:2742968/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:1796768/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATg                                                        >  1:1715933/1‑60 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGaa                                               >  1:1809636/1‑69 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGaa                                               >  1:1978969/1‑69 (MQ=255)
             ccGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGaa                                               >  1:3425495/1‑69 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:354249/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:1490383/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:2610859/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:2437997/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:741361/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:571744/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:127183/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:7564/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:3336963/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:567893/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:1689318/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:1214510/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:932823/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:1859420/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:3205016/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:2884317/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAcc                                        >  1:1778379/1‑68 (MQ=255)
                     ttCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAAc                                         >  1:2896303/1‑67 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCTAAGCCa                                           <  1:442816/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:1413499/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:2554636/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:2657809/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:489182/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:2147168/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:2859606/52‑1 (MQ=255)
                                  cGTGAAGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCa                                           <  1:2908270/52‑1 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTgcgc                          >  1:2335650/1‑68 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:493902/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:3418277/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:3179957/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:488653/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:886745/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:1903247/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:2355387/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         >  1:237940/1‑69 (MQ=255)
                                   gTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCATGCGCt                         >  1:981327/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAATCTCAACAGCCTGCGCTTAt                      >  1:259879/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:2796357/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:1356157/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:675053/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:1788245/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:1804864/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:1257725/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:43559/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:1117654/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:900897/1‑69 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         <  1:3332570/66‑1 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         <  1:3060245/66‑1 (MQ=255)
                                      aaGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         <  1:3130118/66‑1 (MQ=255)
                                      aaGGGAATAAAATTCGTGGTCTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTAt                      >  1:2277304/1‑69 (MQ=255)
                                             tAAAGTTCGTTGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCt                         <  1:212780/59‑1 (MQ=255)
                                                aGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAAt            >  1:271000/1‑69 (MQ=255)
                                                  ttCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATgg          <  1:1573385/69‑1 (MQ=255)
                                                    cGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGGGCTTATTGAATGAAATgg          >  1:842024/1‑67 (MQ=255)
                                                    cGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATgg          >  1:2742934/1‑67 (MQ=255)
                                                    cGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATgg          >  1:426218/1‑67 (MQ=255)
                                                    cGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATgg          >  1:1171590/1‑67 (MQ=255)
                                                        gTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATGGCAcagc    >  1:2781872/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATtg                    >  1:1870174/1‑51 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATgg          >  1:818583/1‑61 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:83838/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:1307410/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:860993/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:1049078/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:1027932/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:1815250/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:472168/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:455867/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:404734/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:357452/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:2138041/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:2771022/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:3136216/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:2941778/1‑69 (MQ=255)
                                                          cTGACGCCGAAAATGCTCACCGAAGCCAACCTCAACAGCCTGCGCTTATTGCATGAAATGGCAcagcag  >  1:2938047/1‑69 (MQ=255)
                                                          cTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATGGCAcagcag  <  1:2953671/69‑1 (MQ=255)
                                                              cacCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATGGCAcagcag  <  1:154030/65‑1 (MQ=255)
                                                               |                                                               
TCTCAACGGCATTCCGCAAGATTCACGGATGCATCGTGAAGGGAATAAAGTTCGTGGTCTGACACCGAAAATGCTTACCGAAGCCAACCTCAACAGCCTGCGCTTATTGAATGAAATGGCACAGCAG  >  minE/2011358‑2011484

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