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 1,341,374 A→G 22.0% G210G (GGT→GGC)  wcaA ← predicted glycosyl transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,341,3740AG22.0% 138.3 / 31.2 104G210G (GGT→GGC) wcaApredicted glycosyl transferase
Reads supporting (aligned to +/- strand):  ref base A (74/7);  new base G (17/6);  total (91/13)
Fisher's exact test for biased strand distribution p-value = 3.63e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

Only 100 of 104 total aligned reads displayed.

TGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACC  >  minE/1341312‑1341440
                                                              |                                                                  
tgCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtg                                                               <  1:1298368/68‑1 (MQ=255)
    tGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          <  1:3147311/69‑1 (MQ=255)
    tGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          <  1:1539297/69‑1 (MQ=255)
    tGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          <  1:2066665/69‑1 (MQ=255)
    tGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          <  1:1336075/69‑1 (MQ=255)
    tGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          <  1:654314/69‑1 (MQ=255)
                ggAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCt                                              >  1:1020898/1‑69 (MQ=255)
                ggAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCt                                              >  1:1049099/1‑69 (MQ=255)
                     tACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGtgattga                                                          >  1:1070945/1‑52 (MQ=255)
                       tccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCGCCGtgattga                                                          <  1:553651/49‑1 (MQ=255)
                       tccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCGCCGtgattga                                                          <  1:3259132/49‑1 (MQ=255)
                       tccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCGCCGtgattga                                                          <  1:3124739/49‑1 (MQ=255)
                       tccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCGCCGtgattga                                                          <  1:1255362/49‑1 (MQ=255)
                       tccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCGCCGtgattga                                                          <  1:2985170/49‑1 (MQ=255)
                                  ttttCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACtt                            >  1:43653/1‑69 (MQ=255)
                                  ttttCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACtt                            >  1:976434/1‑69 (MQ=255)
                                  ttttCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACtt                            >  1:2264907/1‑69 (MQ=255)
                                              aGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGAGTCGCCTCTTCTACTTTCCACGGTTCGc                <  1:3201888/69‑1 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCg                                        >  1:2948342/1‑43 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGc                                       >  1:366444/1‑44 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGcc               >  1:339740/1‑68 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:443295/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:1406661/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:2491763/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:5475/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:2548594/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:2976091/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:177184/1‑69 (MQ=255)
                                                gTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:1641636/1‑69 (MQ=255)
                                                gTGATCTGCAATTCACCGTGATTGATATGCAGGATCTGCGTCGc                                       >  1:1689686/1‑44 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTGCACGGTTCGCCGTa            >  1:3423517/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGt             >  1:581454/1‑68 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGt             >  1:786539/1‑68 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:976208/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:1124606/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:250933/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:603062/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:635984/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:711856/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:691225/1‑69 (MQ=255)
                                                  gATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTAGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:1975037/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTc                          >  1:3261401/1‑54 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGc                >  1:1103799/1‑64 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTa            >  1:2061288/1‑68 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:2002160/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:2610203/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:1573874/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:494606/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:2705143/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:2777104/1‑69 (MQ=255)
                                                   aTCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc           >  1:1207761/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCtcttct                                >  1:1317789/1‑46 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGtt                   >  1:751712/1‑59 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:635823/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:3151705/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:1826691/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:249609/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:2955262/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:431753/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg              >  1:2066583/1‑64 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACt          >  1:266610/1‑68 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:640588/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:371430/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:518112/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:1561117/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:3389231/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:2194388/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:2980338/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:293719/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:2672746/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:2513498/1‑69 (MQ=255)
                                                     cTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc         >  1:1845306/1‑69 (MQ=255)
                                                       gCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTc                          >  1:760392/1‑50 (MQ=255)
                                                       gCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTcc        >  1:2602484/1‑68 (MQ=255)
                                                       gCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTcc        >  1:2538770/1‑68 (MQ=255)
                                                       gCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTcc        >  1:25371/1‑68 (MQ=255)
                                                       gCATTACACCGTGATAGATATGCAGGAACTGCGTCGCctcta                                  >  1:604647/1‑41 (MQ=25)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCGACTTTCCACGGTTCGCCg              >  1:2826913/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCAc                              >  1:1492146/1‑45 (MQ=38)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1890135/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:2230988/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:692060/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:772460/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1624842/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:973828/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1086678/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1429117/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1236393/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:2338075/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:2811214/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:1252019/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCACGGTTCGCCg              >  1:3243428/1‑61 (MQ=255)
                                                        cATTTCGCCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCCACTTTCCAAGGTTCGCCg              >  1:1639953/1‑61 (MQ=38)
                                                          tttCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccacc     >  1:1247072/1‑68 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACgg                     >  1:767352/1‑50 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccaccacc  >  1:1928415/1‑69 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccaccacc  >  1:694611/1‑69 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccaccacc  >  1:734359/1‑69 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccaccacc  >  1:586724/1‑69 (MQ=255)
                                                            tCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccaccacc  >  1:2745658/1‑69 (MQ=255)
                                                              |                                                                  
TGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACC  >  minE/1341312‑1341440

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