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 1,134,975 T→G 50.1% A305A (GCT→GCG)  pfkB → 6‑phosphofructokinase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,134,9750TG50.1% 15.6 / 109.8 100A305A (GCT→GCG) pfkB6‑phosphofructokinase II
Reads supporting (aligned to +/- strand):  ref base T (28/22);  new base G (33/17);  total (61/39)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGCAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCATCACCAACCTGTCGGCA  >  minE/1134910‑1135038
                                                                  |                                                               
aGTGCAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTAc                                                              <  1:2864480/69‑1 (MQ=255)
aGTGCAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTAc                                                              <  1:2459310/69‑1 (MQ=255)
aGTGCAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTAc                                                              <  1:2455424/69‑1 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:1133640/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:3033584/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2988986/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2961855/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2569588/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2267035/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2237425/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:2205899/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:1705146/1‑69 (MQ=255)
    cAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCttt                                                          >  1:1630557/1‑69 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTTCGCGTACCttt                                                          >  1:2918282/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTGCGCGTACCttt                                                          >  1:2922207/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:1314452/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:1435569/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:3134046/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:724271/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:3183944/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:1535980/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:1943008/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:2803302/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCttt                                                          >  1:2624846/1‑65 (MQ=255)
        cacaCTCAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTAAGCGTACCttt                                                          >  1:343078/1‑65 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:2817065/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:1024998/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:408335/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:718639/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:1783615/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTa                                                   >  1:1788760/1‑68 (MQ=255)
            cTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTAACCTTTCCCGCTa                                                   >  1:2805931/1‑68 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCTTGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:3004209/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1997102/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2923810/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1260874/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1735143/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:850778/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2282932/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:3211976/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:3425308/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1910738/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1938212/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2140151/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2077283/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2648244/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:2889600/60‑1 (MQ=255)
              cAACCAGGGAACACGCCTGTGCTCCCATCACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:1974878/60‑1 (MQ=255)
                accAGGGAACACGCCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCGTACCTTTc                                                         <  1:666530/56‑1 (MQ=255)
                      gAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACAtt                                        >  1:2856886/1‑69 (MQ=255)
                      gAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACAtt                                        >  1:1565913/1‑69 (MQ=255)
                      gAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACAtt                                        >  1:1574566/1‑69 (MQ=255)
                         cacGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACaaaaa                                            <  1:2542910/62‑1 (MQ=255)
                         cacGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACaaaaa                                            <  1:3164834/62‑1 (MQ=255)
                          acGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACaaaaa                                            <  1:1951688/61‑1 (MQ=255)
                          acGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACaaaaa                                            <  1:943410/61‑1 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:435521/1‑68 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:502518/1‑68 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:62828/1‑68 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:1621577/1‑68 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:2058164/1‑68 (MQ=255)
                            gTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTccccc                                   >  1:2273479/1‑68 (MQ=255)
                             tCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAg                                 <  1:3433634/69‑1 (MQ=255)
                             tCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAg                                 <  1:945744/69‑1 (MQ=255)
                             tCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAg                                 <  1:929635/69‑1 (MQ=255)
                              cTGTGCTCCCATGACGATACGCAAAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAg                                 <  1:337333/69‑1 (MQ=255)
                                   cTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTgg                           <  1:807814/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:1618552/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:1978097/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:233689/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:335891/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:3295927/69‑1 (MQ=255)
                                          gACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatc                    <  1:2126256/69‑1 (MQ=255)
                                             gATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatcat                  <  1:1779655/68‑1 (MQ=255)
                                             gATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatcat                  <  1:2145869/68‑1 (MQ=255)
                                             gATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatcat                  <  1:3415701/68‑1 (MQ=255)
                                             gATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAatcat                  <  1:2439107/68‑1 (MQ=255)
                                                aCGC‑AAAAAATTTACGCTTAGCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCATCAcc              >  1:3127344/1‑69 (MQ=255)
                                                aCGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCATCAcc              >  1:2085939/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCgg    >  1:1397791/1‑68 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCgg    >  1:2028928/1‑68 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:1980232/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:767426/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:1782533/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:152296/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:907077/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:922261/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:982243/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:431685/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:3227731/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:1445465/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2328347/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2330178/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:1258132/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2949790/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:1344222/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2621251/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2736710/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCCGCTAA‑AAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGCa  >  1:2807365/1‑69 (MQ=255)
                                                            ttACGCGTACCTTTCCAGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCACCACCAACCTGTCGGc   >  1:2381112/1‑69 (MQ=255)
                                                                  |                                                               
AGTGCAGCCACACTCAATCAGGGAACACGTCTGTGCTCCCATGACGATACGC‑AAAAAATTTACGCTTACCTTTCCCGCTAACAAAAACATTCCCCCAGCATTGGGGGAATCATCACCAACCTGTCGGCA  >  minE/1134910‑1135038

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