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 949,625 G→C 30.0% P404P (CCC→CCG)  dos ← cAMP phosphodiesterase, heme‑regulated

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE949,6250GC30.0% 152.6 / 82.3 123P404P (CCC→CCG) doscAMP phosphodiesterase, heme‑regulated
Reads supporting (aligned to +/- strand):  ref base G (35/51);  new base C (18/19);  total (53/70)
Fisher's exact test for biased strand distribution p-value = 4.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

Only 100 of 124 total aligned reads displayed.

GGCCCACGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGATTTGGCA  >  minE/949559‑949686
                                                                  |                                                             
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACCCCACCGgagaga                                                        >  1:3063149/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:3276700/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1106157/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:856111/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:238484/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1189140/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1210437/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:560493/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:2060100/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:2679464/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:3386843/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1837822/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:2829446/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1750246/1‑69 (MQ=255)
     aCGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACCGgagaga                                                        >  1:1666321/1‑69 (MQ=255)
            gCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGCCGGCttt                                                 >  1:1770171/1‑69 (MQ=255)
            gCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCttt                                                 >  1:1601497/1‑69 (MQ=255)
            gCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCttt                                                 >  1:2437947/1‑69 (MQ=255)
                  gCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:2282241/1‑67 (MQ=255)
                  gCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:1276946/1‑67 (MQ=255)
                       caatcaCATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGt                                      >  1:116044/1‑69 (MQ=255)
                       caatcaCATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGt                                      >  1:65296/1‑69 (MQ=255)
                       caatcaCATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGt                                      >  1:1675464/1‑69 (MQ=255)
                       caatcaCATCATGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGt                                      >  1:337570/1‑69 (MQ=255)
                           cacaTCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCa                                    >  1:2148525/1‑67 (MQ=255)
                           cacaTCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCa                                    >  1:2841467/1‑67 (MQ=255)
                           cacaTCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCa                                    >  1:1814460/1‑67 (MQ=255)
                            acaTCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCg                                 >  1:2509773/1‑69 (MQ=255)
                            acaTCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCg                                 >  1:745070/1‑69 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:2959549/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:3367749/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:2271332/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:3299757/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:1539888/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:445022/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:1269199/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:1989035/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:69869/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:808173/69‑1 (MQ=255)
                              aTCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:2784063/69‑1 (MQ=255)
                               tCCTTAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:129717/68‑1 (MQ=255)
                               tCCTGAATATGGTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:2197232/68‑1 (MQ=255)
                                    aaTATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTc                                     <  1:2922994/57‑1 (MQ=255)
                                     atatGGTAAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:2480539/62‑1 (MQ=255)
                                      tatGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCTAGGTATTtgt                       <  1:2137538/69‑1 (MQ=255)
                                       atGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATtgt                       <  1:908123/68‑1 (MQ=255)
                                       atGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATtgt                       <  1:1172965/68‑1 (MQ=255)
                                       atGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATtgt                       <  1:1363410/68‑1 (MQ=255)
                                        tGGTCAACACCTATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGc                     >  1:1904891/1‑69 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTc                                              >  1:2481616/1‑44 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:2292812/1‑45 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:1483068/1‑45 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:669174/1‑45 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCg                                             >  1:605403/1‑45 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:2382674/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:3083356/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:1825363/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:1867022/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:2748717/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGt                             >  1:384762/1‑61 (MQ=255)
                                        tGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGc                     >  1:121074/1‑69 (MQ=255)
                                          gTCAACACCGATGAGATACACCACCGGAGAGACGGCTTTGTCGACCAGGTCATCGAg                               <  1:1850344/57‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:3399854/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:675108/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:3317606/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:598868/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:577990/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:43606/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:98933/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:407922/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:30826/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:1055307/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:1803204/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:1815720/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:188648/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:1965948/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:207328/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:211839/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:2682028/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:3232740/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:2811488/69‑1 (MQ=255)
                                            cAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:2876470/69‑1 (MQ=255)
                                                   gATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCACCGAGGTAATTGTGCAGGt                 <  1:1131076/62‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:2774513/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:752777/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:1729753/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:1746068/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:2866955/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:3317761/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:3325672/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:2852547/69‑1 (MQ=255)
                                                      gagaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:2766659/69‑1 (MQ=255)
                                                       agaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTa                            <  1:719181/47‑1 (MQ=255)
                                                       agaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTa                            <  1:142248/47‑1 (MQ=255)
                                                       agaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:841798/68‑1 (MQ=255)
                                                       agaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:2237283/68‑1 (MQ=255)
                                                       agaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGAtt       <  1:1031356/68‑1 (MQ=255)
                                                        gaTACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGt                 <  1:1548920/57‑1 (MQ=255)
                                                           acacCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGATTTGGCa  <  1:1839631/69‑1 (MQ=255)
                                                                acGGGAGAGACGGCTTTGTCGACCAGGGCATCGAGGTAATtgt                       <  1:2114913/43‑1 (MQ=255)
                                                                  |                                                             
GGCCCACGCATAGCCAAGGCTATCAATCACATCCTGAATATGGTCAACACCGATGAGATACACCACGGGAGAGACGGCTTTGTCGACCAGGTCATCGAGGTAATTGTGCAGGTTATTGCGATTTGGCA  >  minE/949559‑949686

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