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 1,050,528 G→A 33.9% A239A (GCG→GCA)  ydhK → conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,050,5280GA33.9% 59.0 / 39.6 77A239A (GCG→GCA) ydhKconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (24/26);  new base A (11/15);  total (35/42)
Fisher's exact test for biased strand distribution p-value = 8.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

TACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACG  >  minE/1050461‑1050590
                                                                   |                                                              
tACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgc                                                               >  1:2507796/1‑69 (MQ=255)
tACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgc                                                               >  1:718423/1‑69 (MQ=255)
tACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgc                                                               >  1:2591594/1‑69 (MQ=255)
tACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgc                                                               >  1:2783207/1‑69 (MQ=255)
 aCTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgcg                                                              >  1:2336133/1‑69 (MQ=255)
 aCTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgcg                                                              >  1:1294749/1‑69 (MQ=255)
 aCTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgcg                                                              >  1:3074093/1‑69 (MQ=255)
 aCTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgcg                                                              >  1:3219885/1‑69 (MQ=255)
 aCTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAcgcgcg                                                              >  1:364897/1‑69 (MQ=255)
       cATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCtt                                                          <  1:3319019/67‑1 (MQ=255)
       cATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCtt                                                          <  1:2169224/67‑1 (MQ=255)
       cATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCtt                                                          <  1:3145273/67‑1 (MQ=255)
       cATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCtt                                                          <  1:1427677/67‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:858470/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:459395/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:1314557/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:2509268/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:2160720/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:715377/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:653823/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:1403584/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:633120/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:151821/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:1598343/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:1594498/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:344071/61‑1 (MQ=255)
            aTTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:337140/61‑1 (MQ=255)
               tgctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCgctgc                                                >  1:2214236/1‑69 (MQ=255)
               tgctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCgctgc                                                >  1:2740534/1‑69 (MQ=255)
               tgctgcGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAAAGCGCGCCTTAATGCgctgc                                                >  1:2070837/1‑69 (MQ=255)
                          cAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCa                                      <  1:3210919/68‑1 (MQ=255)
                          cAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCa                                      <  1:1764449/68‑1 (MQ=255)
                          cAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCa                                      <  1:773931/68‑1 (MQ=255)
                          cAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCa                                      <  1:2580219/68‑1 (MQ=255)
                           aGGCTTTCTTGAGCCACTATCGTTTTCGCCAGCAAAACGCACGCCt                                                           <  1:1622718/46‑1 (MQ=39)
                             gCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCTGCAATTa                                  >  1:1382588/1‑69 (MQ=255)
                             gCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTa                                  <  1:2177058/69‑1 (MQ=255)
                             gCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTa                                  <  1:2779139/69‑1 (MQ=255)
                               tttCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:3413045/69‑1 (MQ=255)
                               tttCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:3343954/69‑1 (MQ=255)
                               tttCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:2326393/69‑1 (MQ=255)
                               tttCTGGAGCCACAATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:1185543/69‑1 (MQ=255)
                               ttgcTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:1040518/66‑1 (MQ=255)
                                ttCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:256689/68‑1 (MQ=255)
                                       gCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGAcc                         <  1:651868/68‑1 (MQ=255)
                                       gCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGAcc                         <  1:1577743/68‑1 (MQ=255)
                                         cACTATCGTTTTCGCCAGCAAAACGCTCGCCTTAATGCGCTGCTCCACCAGCAATTACg                                <  1:1773490/59‑1 (MQ=255)
                                         cACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAgt                      <  1:1325565/69‑1 (MQ=255)
                                         cACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAgt                      <  1:1509965/69‑1 (MQ=255)
                                         cACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAgt                      <  1:1532402/69‑1 (MQ=255)
                                          aCTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCATCa                                      <  1:1375529/52‑1 (MQ=255)
                                            tATCGTTTTCGCCAGCAAAACGGGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTc                   <  1:2377580/69‑1 (MQ=255)
                                            tATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTc                   <  1:186997/69‑1 (MQ=255)
                                            tATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTc                   <  1:2912015/69‑1 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTTCTCCACCAGCAATTACGTATGACCAGTGTCa                  >  1:1449707/1‑69 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:1702013/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:2516212/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:1593796/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:1415515/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:3124288/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:121667/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:775424/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAAt                                    >  1:2805342/1‑51 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTc                   >  1:749752/1‑68 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCa                  >  1:1974826/1‑69 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCa                  >  1:3006969/1‑69 (MQ=255)
                                             aTCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCa                  >  1:1567699/1‑69 (MQ=255)
                                              tCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCAt                 >  1:700016/1‑69 (MQ=255)
                                              tCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCAt                 >  1:692691/1‑69 (MQ=255)
                                              tCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCAt                 >  1:2347734/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCCCCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:2134789/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGc      >  1:60587/1‑68 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:2445742/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:2376164/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:585850/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:539829/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:464296/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:2097200/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:1599598/1‑69 (MQ=255)
                                                          gCAAAACGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:1728205/1‑69 (MQ=255)
                                                          gCAAAAAGCACGCCTTAATGCGCTACTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCg     >  1:1616/1‑69 (MQ=255)
                                                            aaaaCGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGa    >  1:2162422/1‑68 (MQ=255)
                                                            aaaaCGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGa    >  1:1355838/1‑68 (MQ=255)
                                                            aaaaCGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGa    >  1:2882740/1‑68 (MQ=255)
                                                            aaaaCGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGa    >  1:2807970/1‑68 (MQ=255)
                                                             aaaCGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACg  <  1:1781308/69‑1 (MQ=255)
                                                                   |                                                              
TACTGACCATGAATTTGCTGCGTATCCAGGCTTTCTGGAGCCACTATCGTTTTCGCCAGCAAAACGCGCGCCTTAATGCGCTGCTCCACCAGCAATTACGTATGACCAGTGTCATCTCCAGCCTGCGACG  >  minE/1050461‑1050590

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