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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,502,353 G→A 39.2% S92L (TCA→TTA)  lrhA ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,502,3530GA39.2% 37.8 / 49.6 51S92L (TCA→TTA) lrhADNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (12/19);  new base A (10/10);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 5.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGCCATGT  >  minE/1502286‑1502421
                                                                   |                                                                    
tAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatg                                                                   <  1:2882616/71‑1 (MQ=255)
 aaGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatga                                                                  >  1:3442978/1‑71 (MQ=255)
   gATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgat                                                                 >  1:3460194/1‑70 (MQ=255)
      cGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAg                                                              >  1:2968255/1‑70 (MQ=255)
       gTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCa                                                            <  1:2565855/71‑1 (MQ=255)
        tATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAg                                                           <  1:3348895/71‑1 (MQ=255)
            ggCAGATTCATCTGAAGCTCCGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                    <  1:2027532/58‑1 (MQ=255)
             gCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGc                                                         <  1:3193434/68‑1 (MQ=255)
                 aTTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcatca                                                  >  1:427670/1‑71 (MQ=255)
                   tCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatgatg                                                                <  1:1747300/55‑1 (MQ=255)
                     aTCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTa                                               <  1:1663730/70‑1 (MQ=255)
                       cTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTcatcat                                                 >  1:1997200/1‑66 (MQ=255)
                        tGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatgat                                                                 >  1:90936/1‑49 (MQ=255)
                          aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTaaa                                             <  1:1025504/67‑1 (MQ=255)
                          aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACg                                          <  1:794961/70‑1 (MQ=255)
                          aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGc                                         <  1:3044298/71‑1 (MQ=255)
                          aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaaa                                             <  1:2887145/67‑1 (MQ=255)
                             cACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAgg                                      <  1:2585504/71‑1 (MQ=255)
                              aCCGATAGTTAATACGCCCTGAAGATTACTGAACATtga                                                                     >  1:2745006/1‑39 (MQ=255)
                                  aTAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                    <  1:2554937/36‑1 (MQ=255)
                                  aTAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAtttt                                 >  1:3348600/1‑71 (MQ=255)
                                   tAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                <  1:2043192/71‑1 (MQ=255)
                                    aGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCt                                                       >  1:482759/1‑47 (MQ=255)
                                     gTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTcc                               <  1:3275329/70‑1 (MQ=255)
                                     gTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTcc                               <  1:1635212/70‑1 (MQ=255)
                                     gTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTcc                               <  1:1171306/70‑1 (MQ=255)
                                         aTACGCCCTGAAGATTACTGAACATTGATGATGAg                                                              >  1:1314621/1‑35 (MQ=255)
                                          tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                         <  1:328207/71‑1 (MQ=255)
                                          tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                         <  1:608308/71‑1 (MQ=255)
                                          tACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                         <  1:3614413/71‑1 (MQ=255)
                                            cGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAg                                       >  1:3712776/1‑55 (MQ=255)
                                                cTGAAGATTACTGAACATTAATGATGAGCAGGCCtcat                                                    <  1:1685418/38‑1 (MQ=255)
                                                 tGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACg                                          >  1:3940255/1‑47 (MQ=255)
                                                 tGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACg                                          >  1:2671234/1‑47 (MQ=255)
                                                   aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                  <  1:303008/53‑1 (MQ=255)
                                                   aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                >  1:2813071/1‑55 (MQ=255)
                                                   aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                  <  1:2574693/69‑1 (MQ=255)
                                                   aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                  >  1:1267536/1‑69 (MQ=255)
                                                   aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                  >  1:264174/1‑69 (MQ=255)
                                                   aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                  >  1:1855429/1‑69 (MQ=255)
                                                   aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                  <  1:942023/69‑1 (MQ=255)
                                                    aGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaagaag               <  1:2157735/71‑1 (MQ=255)
                                                    aGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaagaag               <  1:3047902/71‑1 (MQ=255)
                                                    aGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaagaag               >  1:2617141/1‑71 (MQ=255)
                                                         aCTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGa           <  1:233059/70‑1 (MQ=255)
                                                          cTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAAt         >  1:1602644/1‑71 (MQ=255)
                                                          cTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAAt         >  1:411082/1‑71 (MQ=255)
                                                           tGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                  <  1:288556/45‑1 (MQ=255)
                                                           tGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                  <  1:1903279/45‑1 (MQ=255)
                                                           tGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg            <  1:3086673/67‑1 (MQ=255)
                                                           tGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAAt         >  1:831882/1‑70 (MQ=255)
                                                           tGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATg        >  1:1536666/1‑71 (MQ=255)
                                                            gAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc       >  1:500620/1‑71 (MQ=255)
                                                            gAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc       >  1:880516/1‑71 (MQ=255)
                                                            gAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc       >  1:9647/1‑71 (MQ=255)
                                                             aaCATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATg        <  1:3377650/69‑1 (MQ=255)
                                                             aaCATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATg        >  1:1491670/1‑69 (MQ=255)
                                                             aaCATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGc       <  1:2756344/70‑1 (MQ=255)
                                                                 ttGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGCCATGt  <  1:3767826/71‑1 (MQ=255)
                                                                   |                                                                    
TAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGCCATGT  >  minE/1502286‑1502421

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