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 2,872,681 G→A 25.1% S51S (AGC→AGT)  yjfY ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,872,6810GA25.1% 123.4 / 34.4 99S51S (AGC→AGT) yjfYhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (35/39);  new base A (12/13);  total (47/52)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

ACGTGGTAGTACGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATATTTCTGG  >  minE/2872622‑2872748
                                                           |                                                                   
aCGTGGTAGTACGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTg                                                            >  1:2717039/1‑69 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:1190805/1‑69 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:1242241/1‑69 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:1341653/1‑69 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:1337689/1‑69 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAt                                                     >  1:291542/1‑68 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:2150991/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:928428/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:1191190/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:2414603/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:490493/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:2565638/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:3077685/69‑1 (MQ=255)
        gtaCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:2725384/69‑1 (MQ=255)
        gtaCGTTGAGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:629691/69‑1 (MQ=255)
        gtaAGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:93374/1‑69 (MQ=255)
         taCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:1647279/68‑1 (MQ=255)
         taCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGtt                                                    <  1:1963330/68‑1 (MQ=255)
         taCGTTGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCCCAGTGGCGAAGtt                                                    <  1:242846/68‑1 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTc                                                                >  1:242706/1‑54 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGaaa                                                      >  1:3286930/1‑64 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAt                                                     >  1:510367/1‑65 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:3265471/1‑69 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:2709407/1‑69 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:3372267/1‑69 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:2181839/1‑69 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:1057561/1‑69 (MQ=255)
           cGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtg                                                 >  1:2110359/1‑69 (MQ=255)
             ttGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGTTAtga                                                >  1:450233/1‑68 (MQ=255)
             ttGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGTTAtga                                                >  1:1045536/1‑68 (MQ=255)
             ttGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGTTAtga                                                >  1:3006730/1‑68 (MQ=255)
             ttGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGTTAtga                                                >  1:2597171/1‑68 (MQ=255)
             ttGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGTGCTTCACTCTCAGTGGCGAAGTTAtga                                                >  1:2177438/1‑68 (MQ=255)
              tGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTAtgatt                                              <  1:863004/69‑1 (MQ=255)
              tGCGCCTTGCGCATCTGTCTCTTCATTTAATGCCTGACGAGCTTCACTCTCAGTGGCTAAGtt                                                    <  1:2232629/63‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:59680/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2923173/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:1428602/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2585095/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:3013352/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:1226709/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2355656/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2320917/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:117831/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:1179133/68‑1 (MQ=255)
                        gcATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2133914/68‑1 (MQ=255)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:312256/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:469495/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:3001534/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:2317325/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:1286925/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAATGCCTGACGTGCTTCACt                                                                   >  1:2199070/1‑35 (MQ=37)
                           tCTGTCTCTTCATTTAAAGCCTGACGTGCTTCACt                                                                   >  1:2772719/1‑35 (MQ=25)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:246409/63‑1 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:66405/63‑1 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:2720772/63‑1 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:1208835/63‑1 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAAt                                     <  1:1698789/63‑1 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:2901691/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:2908568/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:944398/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:1747726/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:3240994/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:732857/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:1283187/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:1644384/1‑68 (MQ=255)
                             tGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGc                                >  1:2318403/1‑68 (MQ=255)
                                 tcttcATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:567052/1‑44 (MQ=255)
                                 tcttcATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAAtt                                                    >  1:1311240/1‑44 (MQ=255)
                                       tttAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:2974835/68‑1 (MQ=255)
                                       tttAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:379325/68‑1 (MQ=255)
                                       tttAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:2617344/68‑1 (MQ=255)
                                       tttAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:1530246/68‑1 (MQ=255)
                                       tttAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:1223476/68‑1 (MQ=255)
                                         tAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGcac                   <  1:3433522/69‑1 (MQ=255)
                                         tAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGcac                   <  1:1484004/69‑1 (MQ=255)
                                         tAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGcac                   <  1:2576697/69‑1 (MQ=255)
                                         tAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGcac                   <  1:1915180/69‑1 (MQ=255)
                                         tAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGaac                   <  1:2653189/69‑1 (MQ=255)
                                             gCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTg                      <  1:1677750/62‑1 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:960014/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:1939841/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:2719108/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:1856157/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:2681614/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:2033400/1‑68 (MQ=255)
                                              ccTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCg               >  1:1718509/1‑68 (MQ=255)
                                                 gACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCa           <  1:1338513/69‑1 (MQ=255)
                                                 gACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCa           <  1:1912290/69‑1 (MQ=255)
                                                 gACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCa           <  1:793926/69‑1 (MQ=255)
                                                 gACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCa           <  1:2104285/69‑1 (MQ=255)
                                                 gACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCa           <  1:1646780/69‑1 (MQ=255)
                                                     tGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATAtt       <  1:121751/69‑1 (MQ=255)
                                                     tGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATAtt       <  1:468866/69‑1 (MQ=255)
                                                     tGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATAtt       <  1:3166054/69‑1 (MQ=255)
                                                     tGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTACATAtt       <  1:2147/69‑1 (MQ=255)
                                                     tGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTACATAtt       <  1:2465248/69‑1 (MQ=255)
                                                      gCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATAtt       <  1:1931902/68‑1 (MQ=255)
                                                          cGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATATTTCTgg  >  1:660633/1‑69 (MQ=255)
                                                           |                                                                   
ACGTGGTAGTACGTTGCGCCTTGCGCATCTGTTTCTTCATTTAATGCCTGACGTGCTTCGCTTTCAGTGGCGAAATTATGATTGATATAAATCACGCCTAAGCTTTGCACATCGTCCATATTTCTGG  >  minE/2872622‑2872748

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