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 1,969,083 G→A 36.1% K59K (AAG→AAA)  yggG → predicted peptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,969,0830GA36.1% 70.6 / 62.4 105K59K (AAG→AAA) yggGpredicted peptidase
Reads supporting (aligned to +/- strand):  ref base G (51/16);  new base A (24/14);  total (75/30)
Fisher's exact test for biased strand distribution p-value = 1.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

Only 100 of 105 total aligned reads displayed.

AGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGC  >  minE/1969021‑1969142
                                                              |                                                           
aGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGcgac                                                        <  1:1968658/68‑1 (MQ=255)
aGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGcgac                                                        <  1:1990900/68‑1 (MQ=255)
aGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGcgac                                                        <  1:1435413/68‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:2850079/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:1906844/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:1888614/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:1823782/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:1815304/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:2131257/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:2718744/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:2897352/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:29211/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:2991797/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:3392692/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:450899/64‑1 (MQ=255)
        tGATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGAtt                                                    <  1:1104304/64‑1 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:1045587/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:3141251/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:266202/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:2597019/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:216827/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:501843/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:542250/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:2003705/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:578339/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:594836/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:944942/1‑69 (MQ=255)
         gATGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:1366852/1‑69 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:3147771/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:83824/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:109581/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:1490780/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:305351/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:1590745/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:3205535/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:2153467/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:267305/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:2670166/1‑68 (MQ=255)
          aTGCGCAGGTGAAAAAACTGAGCGATCAGGCATGCCAGGAGATGGACAGCAAAGCGACGATTGCgcca                                              >  1:2627907/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                           >  1:3185222/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                           >  1:2410956/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                           >  1:2978034/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                           >  1:1828444/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcc                                           >  1:1372812/1‑68 (MQ=255)
             cgcAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                              >  1:2272316/1‑65 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcca                                          >  1:2402918/1‑63 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAg                                      >  1:1267775/1‑67 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGc                                     >  1:1343955/1‑68 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:1868184/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:3312044/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:3393068/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:2632556/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:1535811/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:1620233/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:2458978/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCg                                    >  1:850942/1‑69 (MQ=255)
                   tGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATAGCGCCAGCCAATAg                                      >  1:2695544/1‑67 (MQ=255)
                                    cAGGCATGTCAGGAGATGGACAGCAAGGCGTCGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCt                    >  1:547388/1‑68 (MQ=255)
                                    cAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcca                                          >  1:329042/1‑46 (MQ=255)
                                    cAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCt                    >  1:2220671/1‑68 (MQ=255)
                                    cAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCt                    >  1:2726558/1‑68 (MQ=255)
                                    cAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCt                    >  1:544244/1‑68 (MQ=255)
                                       gCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                 <  1:54892/68‑1 (MQ=255)
                                       gCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                 <  1:2348821/68‑1 (MQ=255)
                                       gCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                 <  1:2537264/68‑1 (MQ=255)
                                       gCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                 <  1:1523749/68‑1 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACaa               >  1:2940602/1‑68 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACaa               >  1:1342550/1‑68 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAAc              >  1:2067420/1‑69 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAAc              >  1:1214470/1‑69 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAAc              >  1:472750/1‑69 (MQ=255)
                                         aTGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAAc              >  1:2597823/1‑69 (MQ=255)
                                            tCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt           >  1:320238/1‑69 (MQ=255)
                                            tCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt           >  1:928289/1‑69 (MQ=255)
                                            tCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt           >  1:2413970/1‑69 (MQ=255)
                                            tCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt           >  1:2830290/1‑69 (MQ=255)
                                            tCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAt           >  1:2721465/1‑69 (MQ=255)
                                                  gaTGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCaa     >  1:889121/1‑69 (MQ=255)
                                                  gaTGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCaa     >  1:2209367/1‑69 (MQ=255)
                                                  gaTGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCaa     >  1:1369611/1‑69 (MQ=255)
                                                  gaTGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCa      >  1:3009970/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:1118374/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:1186687/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:686381/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:1043997/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:1267843/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:3241530/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:3136939/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:2477633/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:2462740/1‑68 (MQ=255)
                                                      gACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgc  >  1:2456709/1‑68 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:363707/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:3178031/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:3000346/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:2749432/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:69797/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:833945/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:2407960/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGcc       <  1:2155428/57‑1 (MQ=255)
                                                            aaGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTAATGcc       <  1:183707/57‑1 (MQ=255)
                                                              |                                                           
AGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGC  >  minE/1969021‑1969142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A